Starting phenix.real_space_refine
on Thu Feb 13 20:28:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/02_2025/9c0f_45082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/02_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_45082/02_2025/9c0f_45082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/02_2025/9c0f_45082.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c0f_45082/02_2025/9c0f_45082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.22, per 1000 atoms: 0.65
  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: 2.70
  Conformation dependent library (CDL) restraints added in 890.0 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: 3.76
  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: 3.57

  Time building geometry restraints manager: 3.05 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:             1.040
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.360
  Find NCS groups from input model:        0.340
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.150
-------------------------------------------------------------------------------
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  : 0.956 
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: 0.3020
  time to fit residues: 50.4536
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  : 1.097 
-------------------------------------------------------------------------------
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 = 0.063226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.049835 restraints weight = 52933.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.051628 restraints weight = 27839.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.052818 restraints weight = 18391.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
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  : 1.056 
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: 0.8050 (mp) cc_final: 0.7572 (mm)
REVERT: D  231 HIS cc_start: 0.5702 (m170) cc_final: 0.5457 (m170)
REVERT: D  382 MET cc_start: 0.9622 (mmm) cc_final: 0.9138 (tpp)
REVERT: D  513 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8586 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 73
  average time/residue: 0.2840
  time to fit residues: 28.5340
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  : 1.088 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.3384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.064425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.051019 restraints weight = 54037.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.052797 restraints weight = 29343.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.054024 restraints weight = 19705.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3581

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= 0.180
  Angle     :  0.642   9.074  13591  Z= 0.354
  Chirality :  0.041   0.175   1455
  Planarity :  0.004   0.033   1470
  Dihedral  : 21.746 168.348   1841
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.66 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.73 %
    Favored  : 91.27 %
  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:  0.93 (0.29), residues: 331
  sheet:  0.73 (0.54), residues: 83
  loop : -0.68 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 138 
 HIS   0.005   0.001   HIS C 231 
 PHE   0.014   0.001   PHE C 445 
 TYR   0.027   0.002   TYR C 312 
 ARG   0.006   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  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.8003 (mp) cc_final: 0.7651 (mm)
REVERT: C  496 MET cc_start: 0.7878 (ttp) cc_final: 0.7644 (ttp)
REVERT: D  382 MET cc_start: 0.9682 (mmm) cc_final: 0.9156 (mmm)
REVERT: D  496 MET cc_start: 0.7683 (tmm) cc_final: 0.6944 (tmm)
REVERT: D  549 MET cc_start: 0.8546 (ttp) cc_final: 0.7602 (tmm)
  outliers start: 9
  outliers final: 4
  residues processed: 67
  average time/residue: 0.2336
  time to fit residues: 22.2013
Evaluate side-chains
  58 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 67 optimal weight:    0.0000
   chunk 3 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    4.7992

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.061281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.047936 restraints weight = 54754.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.049563 restraints weight = 30868.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.050605 restraints weight = 21197.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9865  Z= 0.305
  Angle     :  0.667   8.998  13591  Z= 0.366
  Chirality :  0.042   0.179   1455
  Planarity :  0.004   0.033   1470
  Dihedral  : 21.643 164.830   1841
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.39 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  7.95 %
    Favored  : 89.81 %
  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: -0.10 (0.27), residues: 956
  helix:  0.95 (0.29), residues: 342
  sheet:  0.51 (0.53), residues: 83
  loop : -0.85 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP D 138 
 HIS   0.005   0.001   HIS C 231 
 PHE   0.021   0.002   PHE C 149 
 TYR   0.029   0.002   TYR C 422 
 ARG   0.007   0.001   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
  75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  513 MET cc_start: 0.8423 (mpp) cc_final: 0.8164 (mmt)
REVERT: D  130 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8713 (ptpp)
REVERT: D  183 MET cc_start: 0.8298 (mtt) cc_final: 0.7993 (mtt)
REVERT: D  356 ARG cc_start: 0.7490 (ptt90) cc_final: 0.7114 (ttp80)
REVERT: D  382 MET cc_start: 0.9663 (mmm) cc_final: 0.9017 (mmm)
REVERT: D  496 MET cc_start: 0.7694 (tmm) cc_final: 0.7214 (tmm)
  outliers start: 20
  outliers final: 15
  residues processed: 66
  average time/residue: 0.2427
  time to fit residues: 22.8346
Evaluate side-chains
  69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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  326 PHE
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  362 LEU
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  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  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:    0.9990
   chunk 92 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0050
   chunk 5 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    2.6002

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.062112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.048721 restraints weight = 54008.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.050394 restraints weight = 30133.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.051501 restraints weight = 20623.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9865  Z= 0.193
  Angle     :  0.604   9.674  13591  Z= 0.327
  Chirality :  0.040   0.140   1455
  Planarity :  0.003   0.033   1470
  Dihedral  : 21.518 166.505   1841
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.97 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.07 %
    Favored  : 89.59 %
  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:  0.05 (0.27), residues: 956
  helix:  1.30 (0.30), residues: 337
  sheet:  0.12 (0.53), residues: 89
  loop : -0.82 (0.26), residues: 530

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   0.012   0.001   PHE C 149 
 TYR   0.026   0.002   TYR C 422 
 ARG   0.003   0.000   ARG D 434 

*********************** 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
  71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 LEU cc_start: 0.9009 (tt) cc_final: 0.8646 (tp)
REVERT: D  183 MET cc_start: 0.8260 (mtt) cc_final: 0.7985 (mtt)
REVERT: D  382 MET cc_start: 0.9669 (mmm) cc_final: 0.9079 (mmm)
REVERT: D  386 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7952 (tt0)
REVERT: D  496 MET cc_start: 0.7648 (tmm) cc_final: 0.7379 (tmm)
REVERT: D  549 MET cc_start: 0.8568 (ttp) cc_final: 0.7638 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 66
  average time/residue: 0.2337
  time to fit residues: 21.9817
Evaluate side-chains
  61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  373 LEU
Chi-restraints excluded: chain C residue  530 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:    3.9990
   chunk 45 optimal weight:    0.0470
   chunk 69 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0060
   chunk 53 optimal weight:    9.9990
   chunk 96 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.4100

-------------------------------------------------------------------------------
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 231 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.063809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.050728 restraints weight = 57136.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.052423 restraints weight = 31794.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.053557 restraints weight = 21677.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9865  Z= 0.160
  Angle     :  0.583  10.766  13591  Z= 0.313
  Chirality :  0.039   0.142   1455
  Planarity :  0.003   0.027   1470
  Dihedral  : 21.410 164.889   1841
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.50 %
    Favored  : 95.40 %
  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:  0.21 (0.27), residues: 956
  helix:  1.42 (0.30), residues: 338
  sheet:  0.78 (0.57), residues: 70
  loop : -0.78 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 138 
 HIS   0.008   0.001   HIS D 231 
 PHE   0.009   0.001   PHE C 461 
 TYR   0.034   0.001   TYR C 422 
 ARG   0.008   0.000   ARG D 356 

*********************** 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
  73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.7809 (mp) cc_final: 0.7055 (tp)
REVERT: C  278 MET cc_start: 0.8412 (ttp) cc_final: 0.7628 (tpp)
REVERT: C  437 MET cc_start: 0.7875 (tpt) cc_final: 0.7563 (ttp)
REVERT: C  513 MET cc_start: 0.8978 (mmt) cc_final: 0.8752 (mmp)
REVERT: D  183 MET cc_start: 0.8202 (mtt) cc_final: 0.7922 (mtt)
REVERT: D  292 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7951 (pt)
REVERT: D  382 MET cc_start: 0.9683 (mmm) cc_final: 0.9069 (mmm)
REVERT: D  386 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7893 (tt0)
REVERT: D  409 MET cc_start: 0.7854 (tpp) cc_final: 0.7612 (mmp)
REVERT: D  549 MET cc_start: 0.8551 (ttp) cc_final: 0.7511 (tmm)
  outliers start: 13
  outliers final: 8
  residues processed: 69
  average time/residue: 0.2427
  time to fit residues: 23.6390
Evaluate side-chains
  67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain D residue  386 GLN
Chi-restraints excluded: chain D residue  413 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0050
   chunk 49 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    2.2002

-------------------------------------------------------------------------------
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**
** D 231 HIS ** 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 = 0.3785 r_free = 0.3785 target = 0.062079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.048619 restraints weight = 55058.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.050315 restraints weight = 30180.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.051455 restraints weight = 20480.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9865  Z= 0.182
  Angle     :  0.582  10.858  13591  Z= 0.312
  Chirality :  0.039   0.139   1455
  Planarity :  0.003   0.040   1470
  Dihedral  : 21.420 162.541   1841
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.29 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.85 %
    Favored  : 88.69 %
  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:  0.21 (0.27), residues: 956
  helix:  1.46 (0.30), residues: 343
  sheet:  0.67 (0.58), residues: 70
  loop : -0.82 (0.26), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 138 
 HIS   0.005   0.001   HIS D 231 
 PHE   0.011   0.001   PHE C 149 
 TYR   0.025   0.001   TYR C 422 
 ARG   0.017   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
  69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  278 MET cc_start: 0.8375 (ttp) cc_final: 0.7566 (tpp)
REVERT: D  183 MET cc_start: 0.8231 (mtt) cc_final: 0.7951 (mtt)
REVERT: D  292 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7980 (pt)
REVERT: D  382 MET cc_start: 0.9676 (mmm) cc_final: 0.9054 (mmm)
REVERT: D  409 MET cc_start: 0.7913 (tpp) cc_final: 0.7695 (mmp)
REVERT: D  549 MET cc_start: 0.8546 (ttp) cc_final: 0.7506 (tmm)
  outliers start: 13
  outliers final: 9
  residues processed: 63
  average time/residue: 0.2351
  time to fit residues: 21.5033
Evaluate side-chains
  64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain D residue  413 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 75 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 80 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   overall best weight:    2.0982

-------------------------------------------------------------------------------
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**
** D 231 HIS ** 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 = 0.3796 r_free = 0.3796 target = 0.062322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.048913 restraints weight = 54793.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.050594 restraints weight = 30333.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.051715 restraints weight = 20608.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9865  Z= 0.171
  Angle     :  0.581  12.135  13591  Z= 0.308
  Chirality :  0.039   0.137   1455
  Planarity :  0.003   0.051   1470
  Dihedral  : 21.359 160.511   1841
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.50 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.74 %
    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:  0.25 (0.28), residues: 956
  helix:  1.59 (0.30), residues: 337
  sheet:  1.15 (0.66), residues: 60
  loop : -0.88 (0.26), residues: 559

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   0.009   0.001   PHE C 149 
 TYR   0.028   0.001   TYR C 422 
 ARG   0.010   0.000   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
  68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  181 LYS cc_start: 0.9168 (mttt) cc_final: 0.8864 (mtpt)
REVERT: C  278 MET cc_start: 0.8384 (ttp) cc_final: 0.7576 (tpp)
REVERT: D  183 MET cc_start: 0.8211 (mtt) cc_final: 0.7962 (mtt)
REVERT: D  382 MET cc_start: 0.9678 (mmm) cc_final: 0.9053 (mmm)
REVERT: D  409 MET cc_start: 0.7807 (tpp) cc_final: 0.7599 (mmp)
REVERT: D  459 MET cc_start: 0.8392 (ptp) cc_final: 0.8071 (ptm)
  outliers start: 11
  outliers final: 8
  residues processed: 64
  average time/residue: 0.2481
  time to fit residues: 22.5298
Evaluate side-chains
  66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:   30.0000
   chunk 5 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0170
   chunk 57 optimal weight:    4.9990
   chunk 79 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   overall best weight:    1.0020

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

Flipped N/Q/H residues before XYZ refinement:
C 313 ASN
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 158 GLN
** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.063493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.050023 restraints weight = 54118.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.051775 restraints weight = 29423.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.052947 restraints weight = 19814.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9865  Z= 0.144
  Angle     :  0.578  11.788  13591  Z= 0.303
  Chirality :  0.038   0.147   1455
  Planarity :  0.003   0.048   1470
  Dihedral  : 21.238 161.031   1841
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.87 %
    Favored  : 96.03 %
  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:  0.32 (0.28), residues: 956
  helix:  1.64 (0.30), residues: 337
  sheet:  1.07 (0.67), residues: 63
  loop : -0.83 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 138 
 HIS   0.004   0.001   HIS C 231 
 PHE   0.009   0.001   PHE C 326 
 TYR   0.026   0.001   TYR D 260 
 ARG   0.012   0.000   ARG C 514 

*********************** 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
  70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  278 MET cc_start: 0.8340 (ttp) cc_final: 0.7529 (tpp)
REVERT: C  356 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6985 (mtt90)
REVERT: D  183 MET cc_start: 0.8113 (mtt) cc_final: 0.7866 (mtt)
REVERT: D  382 MET cc_start: 0.9686 (mmm) cc_final: 0.9055 (mmm)
REVERT: D  549 MET cc_start: 0.8573 (ttp) cc_final: 0.7894 (tmm)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.2613
  time to fit residues: 23.8469
Evaluate side-chains
  64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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  356 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 50 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 54 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    2.8586

-------------------------------------------------------------------------------
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 231 HIS ** 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 = 0.3800 r_free = 0.3800 target = 0.062905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.049786 restraints weight = 58253.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.051465 restraints weight = 32394.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.052596 restraints weight = 22100.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9865  Z= 0.202
  Angle     :  0.607  12.592  13591  Z= 0.319
  Chirality :  0.039   0.137   1455
  Planarity :  0.003   0.036   1470
  Dihedral  : 21.250 159.843   1841
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.50 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.19 %
    Favored  : 88.69 %
  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:  0.30 (0.28), residues: 956
  helix:  1.68 (0.31), residues: 336
  sheet:  0.96 (0.64), residues: 70
  loop : -0.89 (0.26), residues: 550

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   0.011   0.001   PHE C 149 
 TYR   0.021   0.001   TYR C 422 
 ARG   0.004   0.000   ARG C 214 

********************** 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
  67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  278 MET cc_start: 0.8439 (ttp) cc_final: 0.7587 (tpp)
REVERT: C  356 ARG cc_start: 0.7217 (mtm180) cc_final: 0.6817 (mtt90)
REVERT: D  183 MET cc_start: 0.8294 (mtt) cc_final: 0.8067 (mtt)
REVERT: D  382 MET cc_start: 0.9668 (mmm) cc_final: 0.9025 (mmm)
REVERT: D  409 MET cc_start: 0.7639 (mmp) cc_final: 0.7422 (mmp)
REVERT: D  549 MET cc_start: 0.8596 (ttp) cc_final: 0.7693 (tmm)
  outliers start: 10
  outliers final: 10
  residues processed: 63
  average time/residue: 0.2508
  time to fit residues: 22.0790
Evaluate side-chains
  66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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  496 MET
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=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:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 83 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 231 HIS ** 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 = 0.3760 r_free = 0.3760 target = 0.061361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.048231 restraints weight = 58337.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.049843 restraints weight = 32706.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.050914 restraints weight = 22507.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9865  Z= 0.282
  Angle     :  0.658  12.679  13591  Z= 0.349
  Chirality :  0.041   0.148   1455
  Planarity :  0.005   0.063   1470
  Dihedral  : 21.338 157.522   1841
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.44 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.64 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.27), residues: 956
  helix:  1.33 (0.30), residues: 342
  sheet:  1.20 (0.69), residues: 60
  loop : -1.08 (0.25), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 431 
 HIS   0.006   0.001   HIS D 231 
 PHE   0.016   0.002   PHE C 220 
 TYR   0.029   0.002   TYR D 260 
 ARG   0.019   0.001   ARG C 514 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3374.43 seconds
wall clock time: 61 minutes 17.03 seconds (3677.03 seconds total)