Starting phenix.real_space_refine
on Wed Jun 11 15:53:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6gj1_0009/06_2025/6gj1_0009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6gj1_0009/06_2025/6gj1_0009.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6gj1_0009/06_2025/6gj1_0009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6gj1_0009/06_2025/6gj1_0009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6gj1_0009/06_2025/6gj1_0009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6gj1_0009/06_2025/6gj1_0009.cif"
  }
  resolution = 4.7
  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=   1.000
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: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    8271      2.51       5
     N    2325      2.21       5
     O    2352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13013
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4655
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 36, 'TRANS': 547}
    Chain: "B"
      Number of atoms: 4651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4651
          Classifications: {'peptide': 583}
          Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 544}
    Chain: "C"
      Number of atoms: 2737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2737
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 320}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 970
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
  Time building chain proxies: 8.35, per 1000 atoms: 0.64
  Number of scatterers: 13013
  At special positions: 0
  Unit cell: (129.8, 111.1, 145.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      65     16.00
     O    2352      8.00
     N    2325      7.00
     C    8271      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.68
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3038

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      27.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 21
    Processing helix  chain 'A' and resid 46 through 66
      removed outlier: 3.655A  pdb=" N   PHE A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLY A  52 " --> pdb=" O   ARG A  48 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 70
    Processing helix  chain 'A' and resid 71 through 77
      removed outlier: 3.557A  pdb=" N   SER A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.777A  pdb=" N   ASP A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 195
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 4.034A  pdb=" N   GLY A 233 " --> pdb=" O   LEU A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
      removed outlier: 4.128A  pdb=" N   GLU A 433 " --> pdb=" O   ASP A 430 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLN A 434 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL A 435 " --> pdb=" O   CYS A 432 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 430 through 435'
    Processing helix  chain 'A' and resid 458 through 471
      removed outlier: 4.103A  pdb=" N   TRP A 462 " --> pdb=" O   ASP A 458 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   GLY A 469 " --> pdb=" O   MET A 465 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   THR A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 484
    Processing helix  chain 'A' and resid 487 through 493
      removed outlier: 4.105A  pdb=" N   ARG A 492 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.746A  pdb=" N   PHE A 544 " --> pdb=" O   ASP A 540 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ASN A 549 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LEU A 552 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 553 " --> pdb=" O   ASN A 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 22
      removed outlier: 4.133A  pdb=" N   ARG B  17 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ALA B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 32
      removed outlier: 3.612A  pdb=" N   ALA B  32 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 46 through 58
      removed outlier: 3.807A  pdb=" N   GLU B  51 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B  56 " --> pdb=" O   GLY B  52 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   MET B  57 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 68
      removed outlier: 3.632A  pdb=" N   ASP B  67 " --> pdb=" O   LYS B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 74
      removed outlier: 3.506A  pdb=" N   GLU B  73 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 86
      removed outlier: 3.541A  pdb=" N   THR B  86 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 197
      removed outlier: 3.596A  pdb=" N   ARG B 197 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 226
      removed outlier: 4.033A  pdb=" N   GLU B 225 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 235
    Processing helix  chain 'B' and resid 236 through 238
      No H-bonds generated for 'chain 'B' and resid 236 through 238'
    Processing helix  chain 'B' and resid 275 through 280
    Processing helix  chain 'B' and resid 329 through 334
    Processing helix  chain 'B' and resid 458 through 469
      removed outlier: 5.189A  pdb=" N   MET B 465 " --> pdb=" O   HIS B 461 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   SER B 466 " --> pdb=" O   TRP B 462 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY B 469 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 483
    Processing helix  chain 'B' and resid 486 through 490
    Processing helix  chain 'B' and resid 494 through 502
    Processing helix  chain 'B' and resid 537 through 553
      removed outlier: 4.184A  pdb=" N   LEU B 543 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLU B 546 " --> pdb=" O   HIS B 542 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   LEU B 548 " --> pdb=" O   PHE B 544 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ASN B 549 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU B 552 " --> pdb=" O   LEU B 548 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ALA B 553 " --> pdb=" O   ASN B 549 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 15
    Processing helix  chain 'C' and resid 22 through 26
      removed outlier: 3.979A  pdb=" N   ILE C  26 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 45 through 51
      removed outlier: 4.218A  pdb=" N   GLN C  50 " --> pdb=" O   SER C  47 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA C  51 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 109
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 118 through 123
    Processing helix  chain 'C' and resid 123 through 139
      removed outlier: 3.635A  pdb=" N   ARG C 128 " --> pdb=" O   ILE C 124 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ILE C 130 " --> pdb=" O   SER C 126 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR C 131 " --> pdb=" O   HIS C 127 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLN C 132 " --> pdb=" O   ARG C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 162
    Processing helix  chain 'C' and resid 179 through 187
      removed outlier: 4.201A  pdb=" N   LEU C 183 " --> pdb=" O   ARG C 179 " (cutoff:3.500A)
      Proline residue:  C 185  - end of helix
    Processing helix  chain 'C' and resid 195 through 205
      removed outlier: 3.572A  pdb=" N   SER C 199 " --> pdb=" O   GLU C 195 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 266
    Processing helix  chain 'C' and resid 273 through 283
      removed outlier: 3.720A  pdb=" N   ASP C 277 " --> pdb=" O   HIS C 273 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU C 282 " --> pdb=" O   LEU C 278 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   HIS C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 43
    Processing helix  chain 'D' and resid 59 through 64
      removed outlier: 3.510A  pdb=" N   LEU D  63 " --> pdb=" O   ILE D  59 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 85
      removed outlier: 3.763A  pdb=" N   GLN D  72 " --> pdb=" O   GLY D  68 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95
    Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342
    Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 514
      removed outlier: 7.895A  pdb=" N   THR A 565 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   VAL A 526 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   ILE A 567 " --> pdb=" O   VAL A 526 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   VAL A 528 " --> pdb=" O   ILE A 567 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 94
    Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 179
      removed outlier: 6.492A  pdb=" N   LEU B 178 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 204
    Processing sheet with id=AA7, first strand: chain 'B' and resid 305 through 307
      removed outlier: 3.880A  pdb=" N   LEU B 307 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE B 412 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG B 411 " --> pdb=" O   THR B 342 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376
    Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510
      removed outlier: 3.858A  pdb=" N   GLN B 508 " --> pdb=" O   ASP B 525 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASP B 525 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   HIS B 510 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 566
    Processing sheet with id=AB2, first strand: chain 'C' and resid 209 through 213
    Processing sheet with id=AB3, first strand: chain 'C' and resid 294 through 295
    Processing sheet with id=AB4, first strand: chain 'D' and resid 88 through 97
      removed outlier: 4.035A  pdb=" N   ARG D  90 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    696 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.20

  Time building geometry restraints manager: 4.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3534
        1.33 -     1.45: 2992
        1.45 -     1.58: 6691
        1.58 -     1.70: 1
        1.70 -     1.82: 109
  Bond restraints: 13327
  Sorted by residual:
  bond pdb=" CA  PRO D 126 "
       pdb=" C   PRO D 126 "
    ideal  model  delta    sigma   weight residual
    1.522  1.466  0.055 1.16e-02 7.43e+03 2.29e+01
  bond pdb=" C   ASN A 582 "
       pdb=" N   PRO A 583 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.054 1.25e-02 6.40e+03 1.88e+01
  bond pdb=" C   HIS C 232 "
       pdb=" N   PRO C 233 "
    ideal  model  delta    sigma   weight residual
    1.336  1.388 -0.052 1.20e-02 6.94e+03 1.88e+01
  bond pdb=" ND1 HIS D  71 "
       pdb=" CE1 HIS D  71 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.43e+01
  bond pdb=" N   PRO D 126 "
       pdb=" CA  PRO D 126 "
    ideal  model  delta    sigma   weight residual
    1.469  1.424  0.046 1.22e-02 6.72e+03 1.41e+01
  ... (remaining 13322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.23: 17222
        3.23 -     6.47: 770
        6.47 -     9.70: 93
        9.70 -    12.94: 10
       12.94 -    16.17: 8
  Bond angle restraints: 18103
  Sorted by residual:
  angle pdb=" N   PRO D 126 "
        pdb=" CA  PRO D 126 "
        pdb=" C   PRO D 126 "
      ideal   model   delta    sigma   weight residual
     110.80   97.05   13.75 1.51e+00 4.39e-01 8.29e+01
  angle pdb=" N   GLY D  68 "
        pdb=" CA  GLY D  68 "
        pdb=" C   GLY D  68 "
      ideal   model   delta    sigma   weight residual
     114.76   99.39   15.37 1.70e+00 3.46e-01 8.17e+01
  angle pdb=" CA  TYR D  84 "
        pdb=" CB  TYR D  84 "
        pdb=" CG  TYR D  84 "
      ideal   model   delta    sigma   weight residual
     113.90  100.36   13.54 1.80e+00 3.09e-01 5.66e+01
  angle pdb=" C   ASP B 557 "
        pdb=" N   MET B 558 "
        pdb=" CA  MET B 558 "
      ideal   model   delta    sigma   weight residual
     121.54  135.23  -13.69 1.91e+00 2.74e-01 5.14e+01
  angle pdb=" C   ARG C 345 "
        pdb=" N   TYR C 346 "
        pdb=" CA  TYR C 346 "
      ideal   model   delta    sigma   weight residual
     121.54  134.89  -13.35 1.91e+00 2.74e-01 4.88e+01
  ... (remaining 18098 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 7378
       16.03 -    32.06: 542
       32.06 -    48.08: 91
       48.08 -    64.11: 13
       64.11 -    80.14: 6
  Dihedral angle restraints: 8030
    sinusoidal: 3302
      harmonic: 4728
  Sorted by residual:
  dihedral pdb=" CA  ARG C 219 "
           pdb=" C   ARG C 219 "
           pdb=" N   ILE C 220 "
           pdb=" CA  ILE C 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -112.59  -67.41     0      5.00e+00 4.00e-02 1.82e+02
  dihedral pdb=" CA  ILE C 220 "
           pdb=" C   ILE C 220 "
           pdb=" N   PRO C 221 "
           pdb=" CA  PRO C 221 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -116.89  -63.11     0      5.00e+00 4.00e-02 1.59e+02
  dihedral pdb=" CA  VAL A 435 "
           pdb=" C   VAL A 435 "
           pdb=" N   LEU A 436 "
           pdb=" CA  LEU A 436 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  120.74   59.26     0      5.00e+00 4.00e-02 1.40e+02
  ... (remaining 8027 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1806
       0.113 -    0.226: 174
       0.226 -    0.338: 15
       0.338 -    0.451: 2
       0.451 -    0.564: 2
  Chirality restraints: 1999
  Sorted by residual:
  chirality pdb=" CA  THR D  43 "
            pdb=" N   THR D  43 "
            pdb=" C   THR D  43 "
            pdb=" CB  THR D  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.96    0.56 2.00e-01 2.50e+01 7.95e+00
  chirality pdb=" CA  ILE D 125 "
            pdb=" N   ILE D 125 "
            pdb=" C   ILE D 125 "
            pdb=" CB  ILE D 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.91    0.52 2.00e-01 2.50e+01 6.78e+00
  chirality pdb=" CA  TYR D  84 "
            pdb=" N   TYR D  84 "
            pdb=" C   TYR D  84 "
            pdb=" CB  TYR D  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 4.97e+00
  ... (remaining 1996 not shown)

  Planarity restraints: 2359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 220 "   -0.086 5.00e-02 4.00e+02   1.30e-01 2.68e+01
        pdb=" N   PRO C 221 "    0.224 5.00e-02 4.00e+02
        pdb=" CA  PRO C 221 "   -0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO C 221 "   -0.068 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "   -0.068 5.00e-02 4.00e+02   1.04e-01 1.72e+01
        pdb=" N   PRO D  67 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  56 "   -0.067 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO D  57 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO D  57 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO D  57 "   -0.056 5.00e-02 4.00e+02
  ... (remaining 2356 not shown)

  Histogram of nonbonded interaction distances:
        0.34 -     1.25: 15
        1.25 -     2.16: 68
        2.16 -     3.08: 8830
        3.08 -     3.99: 33618
        3.99 -     4.90: 57264
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 99795
  Sorted by model distance:
  nonbonded pdb=" N   PRO A  44 "
            pdb=" NE  ARG D  87 "
     model   vdw
     0.341 3.200
  nonbonded pdb=" N   PRO C  99 "
            pdb=" NH2 ARG D  39 "
     model   vdw
     0.378 3.200
  nonbonded pdb=" CG  PRO A  44 "
            pdb=" NH1 ARG D  87 "
     model   vdw
     0.387 3.520
  nonbonded pdb=" CZ  ARG A  48 "
            pdb=" CA  TYR D  84 "
     model   vdw
     0.572 2.960
  nonbonded pdb=" OE2 GLU D  26 "
            pdb=" CD1 LEU D 131 "
     model   vdw
     0.762 3.460
  ... (remaining 99790 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 'A' and resid 4 through 586)
  selection = chain 'B'
}

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:             0.490
  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:          0.580
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     33.230
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
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      :  0.014   0.901  13329  Z= 1.071
  Angle     :  1.510  16.172  18103  Z= 0.857
  Chirality :  0.074   0.564   1999
  Planarity :  0.011   0.130   2359
  Dihedral  : 11.649  80.140   4992
  Min Nonbonded Distance : 0.341

Molprobity Statistics.
  All-atom Clashscore : 23.90
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 18.28 %
    Favored  : 81.35 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.30 %
    Favored  : 93.99 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.81 %
    Twisted General : 1.57 %

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: -5.15 (0.17), residues: 1630
  helix: -3.20 (0.20), residues: 381
  sheet: -2.95 (0.31), residues: 231
  loop : -3.84 (0.16), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.005   TRP B 389 
 HIS   0.025   0.004   HIS B 510 
 PHE   0.032   0.004   PHE B 255 
 TYR   0.039   0.004   TYR B 240 
 ARG   0.024   0.002   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23923 (  262)
  hydrogen bonds       : angle       8.63152 (  696)
  covalent geometry    : bond        0.01032 (13327)
  covalent geometry    : angle       1.50971 (18103)
  Misc. bond           : bond        0.73815 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 280
  time to evaluate  : 1.629 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.9404 (ttt180) cc_final: 0.9121 (ttp-110)
REVERT: A   55 PHE cc_start: 0.8755 (m-10) cc_final: 0.8528 (m-10)
REVERT: A   57 MET cc_start: 0.9064 (mmm) cc_final: 0.8687 (mmm)
REVERT: A  194 MET cc_start: 0.7907 (tpp) cc_final: 0.7459 (tpt)
REVERT: A  256 VAL cc_start: 0.8402 (t) cc_final: 0.7665 (m)
REVERT: A  364 MET cc_start: 0.6897 (mtt) cc_final: 0.6534 (mtt)
REVERT: A  385 MET cc_start: 0.6591 (mtt) cc_final: 0.5625 (mtt)
REVERT: A  401 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8545 (mmt180)
REVERT: A  465 MET cc_start: 0.8226 (mmm) cc_final: 0.7588 (mmm)
REVERT: A  515 PHE cc_start: 0.8437 (t80) cc_final: 0.8151 (t80)
REVERT: A  525 ASP cc_start: 0.8444 (m-30) cc_final: 0.7071 (m-30)
REVERT: A  582 ASN cc_start: 0.7075 (m-40) cc_final: 0.6472 (m-40)
REVERT: B   13 MET cc_start: 0.9005 (ttp) cc_final: 0.8483 (tpt)
REVERT: B   55 PHE cc_start: 0.7639 (m-10) cc_final: 0.7357 (m-80)
REVERT: B   80 TRP cc_start: 0.8098 (t-100) cc_final: 0.7315 (t-100)
REVERT: B  321 TYR cc_start: 0.9315 (p90) cc_final: 0.9009 (p90)
REVERT: B  397 TRP cc_start: 0.7166 (t-100) cc_final: 0.6946 (t-100)
REVERT: B  402 MET cc_start: 0.8375 (mmm) cc_final: 0.8045 (tpp)
REVERT: B  474 ASN cc_start: 0.8500 (m-40) cc_final: 0.8231 (t0)
REVERT: B  551 PHE cc_start: 0.8511 (m-10) cc_final: 0.7702 (m-80)
REVERT: B  565 THR cc_start: 0.7144 (t) cc_final: 0.6843 (t)
REVERT: B  577 TRP cc_start: 0.6702 (m-10) cc_final: 0.6271 (m-10)
REVERT: C   14 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7957 (ttt180)
REVERT: C   64 MET cc_start: 0.2043 (mtt) cc_final: 0.0857 (mmt)
REVERT: C  120 ASP cc_start: 0.8858 (m-30) cc_final: 0.8415 (m-30)
REVERT: C  135 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.7710 (mmt180)
REVERT: C  142 TYR cc_start: 0.8588 (t80) cc_final: 0.8245 (t80)
REVERT: C  242 MET cc_start: 0.8652 (pmt) cc_final: 0.8348 (pmm)
REVERT: C  250 ASN cc_start: 0.8780 (m-40) cc_final: 0.8238 (m110)
REVERT: D   40 ILE cc_start: 0.7716 (pt) cc_final: 0.7365 (pt)
REVERT: D   48 LEU cc_start: 0.7797 (tt) cc_final: 0.7540 (mt)
  outliers start: 10
  outliers final: 2
  residues processed: 288
  average time/residue: 0.3673
  time to fit residues: 138.6585
Evaluate side-chains
  180 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 68 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 127 optimal weight:    6.9990
   chunk 49 optimal weight:    0.5980
   chunk 77 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 148 optimal weight:    7.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
B 208 ASN
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS
B 582 ASN
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 ASN
C 111 GLN
C 127 HIS
C 132 GLN
** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 318 GLN
C 328 GLN
C 350 GLN
C 352 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.075503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.059872 restraints weight = 104598.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.061331 restraints weight = 71142.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.062398 restraints weight = 53076.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098  13329  Z= 0.206
  Angle     :  0.938  13.148  18103  Z= 0.484
  Chirality :  0.052   0.580   1999
  Planarity :  0.009   0.142   2359
  Dihedral  :  9.311  56.909   1829
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 21.82
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 15.64 %
    Favored  : 84.17 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.15 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 2.86 %
    Twisted General : 1.05 %

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: -4.79 (0.18), residues: 1630
  helix: -2.76 (0.20), residues: 409
  sheet: -2.41 (0.36), residues: 185
  loop : -3.75 (0.17), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 137 
 HIS   0.010   0.001   HIS B 510 
 PHE   0.020   0.002   PHE B  50 
 TYR   0.028   0.002   TYR C 346 
 ARG   0.012   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05624 (  262)
  hydrogen bonds       : angle       6.85699 (  696)
  covalent geometry    : bond        0.00443 (13327)
  covalent geometry    : angle       0.93790 (18103)
  Misc. bond           : bond        0.02078 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 231
  time to evaluate  : 1.554 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.9102 (m90) cc_final: 0.8750 (m90)
REVERT: A   57 MET cc_start: 0.9090 (mmm) cc_final: 0.8732 (mmm)
REVERT: A  104 MET cc_start: 0.8871 (mmt) cc_final: 0.8579 (mmm)
REVERT: A  194 MET cc_start: 0.7872 (tpp) cc_final: 0.7598 (tpt)
REVERT: A  256 VAL cc_start: 0.8656 (t) cc_final: 0.8078 (m)
REVERT: A  364 MET cc_start: 0.6794 (mtt) cc_final: 0.6195 (mtt)
REVERT: A  385 MET cc_start: 0.6968 (mtt) cc_final: 0.5657 (mtt)
REVERT: A  402 MET cc_start: 0.9194 (mtm) cc_final: 0.8651 (mtm)
REVERT: A  580 ASN cc_start: 0.9143 (p0) cc_final: 0.8476 (p0)
REVERT: A  582 ASN cc_start: 0.7503 (m-40) cc_final: 0.6855 (m110)
REVERT: B   13 MET cc_start: 0.9012 (ttp) cc_final: 0.8335 (tpt)
REVERT: B   27 HIS cc_start: 0.9094 (t70) cc_final: 0.8868 (t70)
REVERT: B   55 PHE cc_start: 0.7591 (m-10) cc_final: 0.7348 (m-80)
REVERT: B   80 TRP cc_start: 0.8080 (t-100) cc_final: 0.7190 (t-100)
REVERT: B  173 LEU cc_start: 0.8981 (mt) cc_final: 0.8669 (mt)
REVERT: B  230 TRP cc_start: 0.7637 (t60) cc_final: 0.7380 (t-100)
REVERT: B  254 MET cc_start: 0.7942 (ttm) cc_final: 0.7566 (ttm)
REVERT: B  330 ASP cc_start: 0.9614 (p0) cc_final: 0.9353 (t0)
REVERT: B  397 TRP cc_start: 0.7129 (t-100) cc_final: 0.6760 (t-100)
REVERT: B  402 MET cc_start: 0.8117 (mmm) cc_final: 0.7199 (mmm)
REVERT: B  462 TRP cc_start: 0.8285 (t-100) cc_final: 0.8000 (t60)
REVERT: B  474 ASN cc_start: 0.8593 (m-40) cc_final: 0.8158 (t0)
REVERT: B  519 PHE cc_start: 0.9005 (m-10) cc_final: 0.8442 (m-80)
REVERT: B  544 PHE cc_start: 0.8981 (t80) cc_final: 0.8325 (t80)
REVERT: B  546 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8810 (mt-10)
REVERT: B  547 MET cc_start: 0.8821 (ptp) cc_final: 0.8054 (mtm)
REVERT: B  551 PHE cc_start: 0.8372 (m-10) cc_final: 0.7206 (m-80)
REVERT: C   14 ARG cc_start: 0.8307 (mtt180) cc_final: 0.8044 (tpt170)
REVERT: C   58 PHE cc_start: 0.7600 (t80) cc_final: 0.6773 (t80)
REVERT: C  138 ARG cc_start: 0.8192 (tmt170) cc_final: 0.7939 (tpt90)
REVERT: C  142 TYR cc_start: 0.8502 (t80) cc_final: 0.7888 (t80)
REVERT: C  147 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8985 (mp0)
REVERT: C  153 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9019 (mmmt)
REVERT: C  164 LEU cc_start: 0.8946 (mt) cc_final: 0.8727 (mt)
REVERT: C  250 ASN cc_start: 0.8451 (m-40) cc_final: 0.7775 (m110)
REVERT: D   66 MET cc_start: 0.1912 (ttt) cc_final: 0.1025 (tpt)
  outliers start: 3
  outliers final: 2
  residues processed: 234
  average time/residue: 0.3537
  time to fit residues: 108.9911
Evaluate side-chains
  171 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 97 optimal weight:    0.0970
   chunk 100 optimal weight:   40.0000
   chunk 74 optimal weight:    3.9990
   chunk 150 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 112 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    4.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 542 HIS
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 GLN
C 328 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.074371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.059272 restraints weight = 107722.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.060588 restraints weight = 74487.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.061594 restraints weight = 56396.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  13329  Z= 0.209
  Angle     :  0.901  13.487  18103  Z= 0.458
  Chirality :  0.050   0.345   1999
  Planarity :  0.008   0.144   2359
  Dihedral  :  8.740  57.376   1829
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 23.47
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 17.85 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.90 %
    Twisted General : 0.92 %

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: -4.50 (0.18), residues: 1630
  helix: -2.42 (0.21), residues: 403
  sheet: -2.46 (0.36), residues: 184
  loop : -3.55 (0.18), residues: 1043

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP C  49 
 HIS   0.011   0.002   HIS A  82 
 PHE   0.015   0.002   PHE B 223 
 TYR   0.028   0.002   TYR B  15 
 ARG   0.016   0.001   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  262)
  hydrogen bonds       : angle       6.68545 (  696)
  covalent geometry    : bond        0.00445 (13327)
  covalent geometry    : angle       0.90051 (18103)
  Misc. bond           : bond        0.01005 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.650 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.9391 (ttt180) cc_final: 0.8951 (ttp-110)
REVERT: A   27 HIS cc_start: 0.9054 (m90) cc_final: 0.8714 (m90)
REVERT: A   50 PHE cc_start: 0.9482 (m-80) cc_final: 0.9144 (m-10)
REVERT: A   57 MET cc_start: 0.9071 (mmm) cc_final: 0.8627 (mmm)
REVERT: A  104 MET cc_start: 0.8901 (mmt) cc_final: 0.8669 (mmm)
REVERT: A  194 MET cc_start: 0.7847 (tpp) cc_final: 0.7432 (tpt)
REVERT: A  401 ARG cc_start: 0.8887 (mtt180) cc_final: 0.8576 (mmt180)
REVERT: A  402 MET cc_start: 0.9192 (mtm) cc_final: 0.8589 (mtm)
REVERT: A  580 ASN cc_start: 0.9079 (p0) cc_final: 0.8336 (p0)
REVERT: A  582 ASN cc_start: 0.7560 (m-40) cc_final: 0.6899 (m110)
REVERT: B   13 MET cc_start: 0.9019 (ttp) cc_final: 0.8335 (tpt)
REVERT: B   27 HIS cc_start: 0.9101 (t70) cc_final: 0.8899 (t70)
REVERT: B   61 ARG cc_start: 0.8804 (mmt180) cc_final: 0.8596 (mmt180)
REVERT: B   80 TRP cc_start: 0.8182 (t-100) cc_final: 0.7638 (t-100)
REVERT: B  254 MET cc_start: 0.8044 (ttm) cc_final: 0.7685 (ttm)
REVERT: B  364 MET cc_start: 0.8238 (ttp) cc_final: 0.8037 (ttp)
REVERT: B  397 TRP cc_start: 0.7200 (t-100) cc_final: 0.6884 (t-100)
REVERT: B  402 MET cc_start: 0.8105 (mmm) cc_final: 0.7147 (mmm)
REVERT: B  519 PHE cc_start: 0.9176 (m-10) cc_final: 0.8650 (m-80)
REVERT: B  544 PHE cc_start: 0.9049 (t80) cc_final: 0.8468 (t80)
REVERT: B  546 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8747 (mt-10)
REVERT: B  547 MET cc_start: 0.8789 (ptp) cc_final: 0.8344 (mtm)
REVERT: B  551 PHE cc_start: 0.8204 (m-10) cc_final: 0.7838 (m-80)
REVERT: C   14 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7935 (tpt170)
REVERT: C   58 PHE cc_start: 0.7610 (t80) cc_final: 0.6808 (t80)
REVERT: C   64 MET cc_start: 0.1215 (mtt) cc_final: 0.0357 (mtt)
REVERT: C  120 ASP cc_start: 0.8786 (m-30) cc_final: 0.8524 (m-30)
REVERT: C  138 ARG cc_start: 0.8455 (tmt170) cc_final: 0.8151 (tpt90)
REVERT: C  142 TYR cc_start: 0.8466 (t80) cc_final: 0.8184 (t80)
REVERT: C  153 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9093 (mmmt)
REVERT: C  250 ASN cc_start: 0.8577 (m-40) cc_final: 0.7865 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.3667
  time to fit residues: 100.2686
Evaluate side-chains
  155 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 158 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 112 optimal weight:    2.9990
   chunk 160 optimal weight:    9.9990
   chunk 149 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 159 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 ASN
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.075371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.059597 restraints weight = 105692.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061027 restraints weight = 72074.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.062093 restraints weight = 54206.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  13329  Z= 0.161
  Angle     :  0.835  14.101  18103  Z= 0.424
  Chirality :  0.048   0.305   1999
  Planarity :  0.008   0.138   2359
  Dihedral  :  8.143  54.704   1829
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 20.28
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 16.32 %
    Favored  : 83.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.90 %
    Twisted General : 0.72 %

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: -4.18 (0.19), residues: 1630
  helix: -2.05 (0.23), residues: 394
  sheet: -2.17 (0.38), residues: 171
  loop : -3.40 (0.18), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  49 
 HIS   0.010   0.001   HIS B 510 
 PHE   0.026   0.002   PHE A 460 
 TYR   0.025   0.002   TYR C 346 
 ARG   0.009   0.001   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  262)
  hydrogen bonds       : angle       6.58331 (  696)
  covalent geometry    : bond        0.00355 (13327)
  covalent geometry    : angle       0.83501 (18103)
  Misc. bond           : bond        0.01055 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.613 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.8978 (m90) cc_final: 0.8724 (m-70)
REVERT: A   50 PHE cc_start: 0.9417 (m-80) cc_final: 0.9132 (m-80)
REVERT: A   57 MET cc_start: 0.9050 (mmm) cc_final: 0.8825 (mmm)
REVERT: A  102 MET cc_start: 0.6766 (tpp) cc_final: 0.6339 (tpp)
REVERT: A  194 MET cc_start: 0.7917 (tpp) cc_final: 0.7704 (tpt)
REVERT: A  253 PHE cc_start: 0.8169 (m-80) cc_final: 0.7921 (m-80)
REVERT: A  402 MET cc_start: 0.9124 (mtm) cc_final: 0.8264 (mtm)
REVERT: A  517 LYS cc_start: 0.9378 (mttt) cc_final: 0.9131 (mtmt)
REVERT: A  542 HIS cc_start: 0.8416 (m90) cc_final: 0.7870 (m170)
REVERT: A  580 ASN cc_start: 0.8986 (p0) cc_final: 0.8519 (p0)
REVERT: A  582 ASN cc_start: 0.7541 (m-40) cc_final: 0.6828 (m110)
REVERT: B   13 MET cc_start: 0.8915 (ttp) cc_final: 0.8388 (tpp)
REVERT: B   27 HIS cc_start: 0.9091 (t70) cc_final: 0.8863 (t70)
REVERT: B   67 ASP cc_start: 0.8357 (p0) cc_final: 0.8151 (p0)
REVERT: B   80 TRP cc_start: 0.8156 (t-100) cc_final: 0.7662 (t-100)
REVERT: B  254 MET cc_start: 0.7967 (ttm) cc_final: 0.7525 (ttm)
REVERT: B  397 TRP cc_start: 0.7139 (t-100) cc_final: 0.6827 (t-100)
REVERT: B  402 MET cc_start: 0.8068 (mmm) cc_final: 0.7155 (mmm)
REVERT: B  474 ASN cc_start: 0.8696 (p0) cc_final: 0.8296 (p0)
REVERT: B  475 MET cc_start: 0.4955 (mtp) cc_final: 0.4624 (mtp)
REVERT: B  519 PHE cc_start: 0.9179 (m-10) cc_final: 0.8724 (m-80)
REVERT: B  544 PHE cc_start: 0.8986 (t80) cc_final: 0.8364 (t80)
REVERT: B  546 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8764 (mt-10)
REVERT: B  547 MET cc_start: 0.8832 (ptp) cc_final: 0.8373 (mtm)
REVERT: B  558 MET cc_start: 0.8864 (mpp) cc_final: 0.8582 (mmp)
REVERT: C  142 TYR cc_start: 0.8372 (t80) cc_final: 0.8137 (t80)
REVERT: C  153 LYS cc_start: 0.9508 (mmpt) cc_final: 0.9131 (mmmt)
REVERT: C  164 LEU cc_start: 0.8751 (mt) cc_final: 0.8235 (mt)
REVERT: C  184 LEU cc_start: 0.9765 (tt) cc_final: 0.9388 (tp)
REVERT: C  222 LEU cc_start: 0.8950 (mt) cc_final: 0.8713 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.3560
  time to fit residues: 96.9371
Evaluate side-chains
  158 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 153 optimal weight:   20.0000
   chunk 39 optimal weight:   20.0000
   chunk 118 optimal weight:    7.9990
   chunk 105 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 124 optimal weight:   10.0000
   chunk 140 optimal weight:   10.0000
   chunk 143 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 146 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 GLN
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 GLN
C 172 ASN
C 328 GLN
D 134 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.073203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.055058 restraints weight = 102915.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.056381 restraints weight = 70953.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.057461 restraints weight = 54554.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13329  Z= 0.208
  Angle     :  0.870  13.734  18103  Z= 0.439
  Chirality :  0.049   0.286   1999
  Planarity :  0.008   0.146   2359
  Dihedral  :  8.114  56.628   1829
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 23.78
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 18.16 %
    Favored  : 81.66 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.58 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.90 %
    Twisted General : 0.65 %

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: -4.05 (0.19), residues: 1630
  helix: -1.80 (0.24), residues: 385
  sheet: -2.40 (0.36), residues: 197
  loop : -3.31 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 389 
 HIS   0.014   0.002   HIS B 510 
 PHE   0.038   0.002   PHE B 551 
 TYR   0.024   0.002   TYR B 240 
 ARG   0.007   0.001   ARG A 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  262)
  hydrogen bonds       : angle       6.57813 (  696)
  covalent geometry    : bond        0.00449 (13327)
  covalent geometry    : angle       0.87007 (18103)
  Misc. bond           : bond        0.00841 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 1.471 
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: 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: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.8846 (m90) cc_final: 0.8543 (m-70)
REVERT: A   57 MET cc_start: 0.9178 (mmm) cc_final: 0.8827 (mmm)
REVERT: A   78 MET cc_start: 0.9011 (mmm) cc_final: 0.8689 (mmm)
REVERT: A  193 MET cc_start: 0.9166 (tpt) cc_final: 0.8939 (tpp)
REVERT: A  402 MET cc_start: 0.9162 (mtm) cc_final: 0.8571 (mtm)
REVERT: A  580 ASN cc_start: 0.9039 (p0) cc_final: 0.8402 (p0)
REVERT: A  582 ASN cc_start: 0.7679 (m-40) cc_final: 0.7005 (m110)
REVERT: B   13 MET cc_start: 0.8880 (ttp) cc_final: 0.8280 (tpp)
REVERT: B   27 HIS cc_start: 0.9080 (t70) cc_final: 0.8853 (t70)
REVERT: B   80 TRP cc_start: 0.8235 (t-100) cc_final: 0.7470 (t-100)
REVERT: B  102 MET cc_start: 0.8608 (mmp) cc_final: 0.8191 (ppp)
REVERT: B  321 TYR cc_start: 0.9374 (p90) cc_final: 0.9158 (p90)
REVERT: B  397 TRP cc_start: 0.7168 (t-100) cc_final: 0.6905 (t-100)
REVERT: B  402 MET cc_start: 0.8108 (mmm) cc_final: 0.7149 (mmm)
REVERT: B  474 ASN cc_start: 0.8785 (p0) cc_final: 0.8387 (p0)
REVERT: B  475 MET cc_start: 0.5076 (mtp) cc_final: 0.4557 (mtp)
REVERT: B  519 PHE cc_start: 0.8967 (m-10) cc_final: 0.8765 (m-80)
REVERT: B  547 MET cc_start: 0.8697 (ptp) cc_final: 0.7287 (ptp)
REVERT: C   33 GLN cc_start: 0.8608 (tt0) cc_final: 0.8363 (tm-30)
REVERT: C  142 TYR cc_start: 0.8438 (t80) cc_final: 0.8137 (t80)
REVERT: C  153 LYS cc_start: 0.9529 (mmpt) cc_final: 0.9202 (mmmt)
REVERT: C  192 ARG cc_start: 0.4419 (mtt-85) cc_final: 0.2068 (mtt-85)
REVERT: C  222 LEU cc_start: 0.8954 (mt) cc_final: 0.8648 (mp)
REVERT: D   97 GLU cc_start: 0.8157 (pp20) cc_final: 0.7877 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 188
  average time/residue: 0.3161
  time to fit residues: 80.0175
Evaluate side-chains
  143 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 108 optimal weight:    8.9990
   chunk 162 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9990
   chunk 91 optimal weight:   20.0000
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 148 optimal weight:   20.0000
   chunk 25 optimal weight:    8.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 GLN
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 GLN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 ASN
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 328 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.072370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.053724 restraints weight = 99311.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.054896 restraints weight = 70496.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.055800 restraints weight = 55372.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.5289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  13329  Z= 0.245
  Angle     :  0.912  13.562  18103  Z= 0.461
  Chirality :  0.051   0.317   1999
  Planarity :  0.008   0.145   2359
  Dihedral  :  8.257  59.131   1829
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 26.09
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 18.59 %
    Favored  : 81.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.90 %
    Twisted General : 0.65 %

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: -4.11 (0.19), residues: 1630
  helix: -1.93 (0.23), residues: 391
  sheet: -2.44 (0.35), residues: 203
  loop : -3.31 (0.18), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 217 
 HIS   0.012   0.002   HIS A  82 
 PHE   0.029   0.003   PHE B 551 
 TYR   0.022   0.002   TYR B 240 
 ARG   0.008   0.001   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04311 (  262)
  hydrogen bonds       : angle       6.78897 (  696)
  covalent geometry    : bond        0.00526 (13327)
  covalent geometry    : angle       0.91189 (18103)
  Misc. bond           : bond        0.00759 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.567 
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: 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: A   27 HIS cc_start: 0.8824 (m90) cc_final: 0.8506 (m-70)
REVERT: A   57 MET cc_start: 0.9182 (mmm) cc_final: 0.8842 (mmm)
REVERT: A   78 MET cc_start: 0.9085 (mmm) cc_final: 0.8810 (mmp)
REVERT: A  193 MET cc_start: 0.9102 (tpt) cc_final: 0.8832 (tpp)
REVERT: A  402 MET cc_start: 0.9006 (mtm) cc_final: 0.8435 (mtm)
REVERT: A  530 LEU cc_start: 0.8900 (tp) cc_final: 0.8666 (tt)
REVERT: A  580 ASN cc_start: 0.9194 (p0) cc_final: 0.8681 (p0)
REVERT: A  582 ASN cc_start: 0.7741 (m110) cc_final: 0.7035 (m110)
REVERT: B   13 MET cc_start: 0.8876 (ttp) cc_final: 0.8281 (tpp)
REVERT: B   27 HIS cc_start: 0.9092 (t70) cc_final: 0.8862 (t70)
REVERT: B   80 TRP cc_start: 0.8243 (t-100) cc_final: 0.7591 (t-100)
REVERT: B  102 MET cc_start: 0.8664 (mmp) cc_final: 0.8105 (ppp)
REVERT: B  321 TYR cc_start: 0.9466 (p90) cc_final: 0.9128 (p90)
REVERT: B  397 TRP cc_start: 0.7215 (t-100) cc_final: 0.6956 (t-100)
REVERT: B  402 MET cc_start: 0.7764 (mmm) cc_final: 0.6972 (mmm)
REVERT: B  474 ASN cc_start: 0.8798 (p0) cc_final: 0.8389 (p0)
REVERT: B  475 MET cc_start: 0.5115 (mtp) cc_final: 0.4563 (mtp)
REVERT: B  519 PHE cc_start: 0.8978 (m-10) cc_final: 0.8696 (m-80)
REVERT: B  543 LEU cc_start: 0.9295 (tp) cc_final: 0.8887 (tp)
REVERT: B  547 MET cc_start: 0.9036 (ptp) cc_final: 0.6956 (mtp)
REVERT: C  142 TYR cc_start: 0.8481 (t80) cc_final: 0.7930 (t80)
REVERT: C  153 LYS cc_start: 0.9545 (mmpt) cc_final: 0.9209 (mmmt)
REVERT: C  192 ARG cc_start: 0.4263 (mtt-85) cc_final: 0.2024 (mtt-85)
REVERT: C  222 LEU cc_start: 0.9083 (mt) cc_final: 0.8806 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.3445
  time to fit residues: 76.7607
Evaluate side-chains
  142 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 131 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 87 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9990
   chunk 137 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0070
   overall best weight:    1.8006

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

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 ASN
A 569 GLN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 581 HIS
C 172 ASN
C 328 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.074889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.057462 restraints weight = 104193.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.058732 restraints weight = 74049.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.059777 restraints weight = 57417.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13329  Z= 0.142
  Angle     :  0.821  14.250  18103  Z= 0.412
  Chirality :  0.049   0.314   1999
  Planarity :  0.007   0.140   2359
  Dihedral  :  8.853 177.530   1829
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 19.66
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 15.83 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.90 %
    Twisted General : 0.65 %

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: -3.88 (0.19), residues: 1630
  helix: -1.63 (0.24), residues: 390
  sheet: -2.07 (0.38), residues: 183
  loop : -3.27 (0.18), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 168 
 HIS   0.010   0.001   HIS B 467 
 PHE   0.036   0.002   PHE B 551 
 TYR   0.021   0.002   TYR C 346 
 ARG   0.024   0.001   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  262)
  hydrogen bonds       : angle       6.36201 (  696)
  covalent geometry    : bond        0.00317 (13327)
  covalent geometry    : angle       0.82106 (18103)
  Misc. bond           : bond        0.00358 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.464 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.8633 (m90) cc_final: 0.8326 (m-70)
REVERT: A   57 MET cc_start: 0.9068 (mmm) cc_final: 0.8502 (mmm)
REVERT: A  193 MET cc_start: 0.8999 (tpt) cc_final: 0.8656 (tpp)
REVERT: A  385 MET cc_start: 0.5197 (ttm) cc_final: 0.4970 (ttm)
REVERT: A  402 MET cc_start: 0.9030 (mtm) cc_final: 0.8420 (mtm)
REVERT: A  542 HIS cc_start: 0.8369 (m90) cc_final: 0.7894 (m170)
REVERT: A  580 ASN cc_start: 0.9132 (p0) cc_final: 0.8624 (p0)
REVERT: A  582 ASN cc_start: 0.7846 (m110) cc_final: 0.7194 (m110)
REVERT: B   13 MET cc_start: 0.8840 (ttp) cc_final: 0.8263 (tpp)
REVERT: B   27 HIS cc_start: 0.9049 (t70) cc_final: 0.8821 (t70)
REVERT: B   80 TRP cc_start: 0.8039 (t-100) cc_final: 0.7311 (t-100)
REVERT: B  102 MET cc_start: 0.8552 (mmp) cc_final: 0.8155 (ppp)
REVERT: B  254 MET cc_start: 0.7441 (ttm) cc_final: 0.6949 (ttm)
REVERT: B  397 TRP cc_start: 0.7110 (t-100) cc_final: 0.6833 (t-100)
REVERT: B  402 MET cc_start: 0.7770 (mmm) cc_final: 0.7009 (mmm)
REVERT: B  474 ASN cc_start: 0.8755 (p0) cc_final: 0.8297 (p0)
REVERT: B  475 MET cc_start: 0.5024 (mtp) cc_final: 0.4454 (mtp)
REVERT: B  519 PHE cc_start: 0.8920 (m-10) cc_final: 0.8644 (m-80)
REVERT: B  544 PHE cc_start: 0.9002 (t80) cc_final: 0.8162 (t80)
REVERT: B  547 MET cc_start: 0.8685 (ptp) cc_final: 0.7825 (mtp)
REVERT: C   64 MET cc_start: 0.1460 (mtt) cc_final: 0.0257 (mtt)
REVERT: C  142 TYR cc_start: 0.8364 (t80) cc_final: 0.7740 (t80)
REVERT: C  153 LYS cc_start: 0.9543 (mmpt) cc_final: 0.9186 (mmmt)
REVERT: C  184 LEU cc_start: 0.9778 (tt) cc_final: 0.9454 (tp)
REVERT: C  192 ARG cc_start: 0.3858 (mtt-85) cc_final: 0.1764 (mtt-85)
REVERT: C  222 LEU cc_start: 0.9003 (mt) cc_final: 0.8707 (mp)
REVERT: D   66 MET cc_start: 0.2736 (ttt) cc_final: 0.2500 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.3292
  time to fit residues: 80.9938
Evaluate side-chains
  153 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0170
   chunk 110 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 108 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    3.0026

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 GLN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 GLN
C 172 ASN
C 245 HIS
C 328 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.074346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.058625 restraints weight = 106093.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.059972 restraints weight = 73732.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.060981 restraints weight = 56196.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.5899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13329  Z= 0.153
  Angle     :  0.814  14.657  18103  Z= 0.407
  Chirality :  0.048   0.295   1999
  Planarity :  0.007   0.139   2359
  Dihedral  :  8.489 166.819   1829
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 20.66
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 16.93 %
    Favored  : 82.94 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.86 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.95 %
    Twisted General : 0.59 %

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: -3.77 (0.19), residues: 1630
  helix: -1.52 (0.24), residues: 388
  sheet: -1.98 (0.38), residues: 185
  loop : -3.20 (0.18), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 230 
 HIS   0.023   0.002   HIS A 375 
 PHE   0.037   0.002   PHE A 355 
 TYR   0.022   0.002   TYR C 346 
 ARG   0.006   0.001   ARG C 345 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  262)
  hydrogen bonds       : angle       6.32016 (  696)
  covalent geometry    : bond        0.00341 (13327)
  covalent geometry    : angle       0.81399 (18103)
  Misc. bond           : bond        0.00348 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 1.638 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.8617 (m90) cc_final: 0.8333 (m-70)
REVERT: A   57 MET cc_start: 0.9056 (mmm) cc_final: 0.8683 (mmm)
REVERT: A  194 MET cc_start: 0.7523 (tpt) cc_final: 0.7290 (tpt)
REVERT: A  332 TYR cc_start: 0.7480 (m-80) cc_final: 0.7270 (m-80)
REVERT: A  385 MET cc_start: 0.5391 (ttm) cc_final: 0.5129 (ttm)
REVERT: A  402 MET cc_start: 0.9095 (mtm) cc_final: 0.8472 (mtm)
REVERT: A  530 LEU cc_start: 0.8794 (tp) cc_final: 0.8536 (tt)
REVERT: A  542 HIS cc_start: 0.8401 (m90) cc_final: 0.7931 (m170)
REVERT: A  580 ASN cc_start: 0.9205 (p0) cc_final: 0.8757 (p0)
REVERT: A  582 ASN cc_start: 0.8076 (m110) cc_final: 0.7394 (m110)
REVERT: B   13 MET cc_start: 0.8814 (ttp) cc_final: 0.8029 (tpp)
REVERT: B   27 HIS cc_start: 0.9056 (t70) cc_final: 0.8832 (t70)
REVERT: B   80 TRP cc_start: 0.8120 (t-100) cc_final: 0.7371 (t-100)
REVERT: B  102 MET cc_start: 0.8623 (mmp) cc_final: 0.8073 (ppp)
REVERT: B  254 MET cc_start: 0.7592 (ttm) cc_final: 0.7389 (ttm)
REVERT: B  397 TRP cc_start: 0.6818 (t-100) cc_final: 0.6608 (t-100)
REVERT: B  402 MET cc_start: 0.7782 (mmm) cc_final: 0.6969 (mmm)
REVERT: B  474 ASN cc_start: 0.8725 (p0) cc_final: 0.8313 (p0)
REVERT: B  475 MET cc_start: 0.4937 (mtp) cc_final: 0.4387 (mtp)
REVERT: B  519 PHE cc_start: 0.8849 (m-10) cc_final: 0.8561 (m-80)
REVERT: B  547 MET cc_start: 0.8781 (ptp) cc_final: 0.7134 (mtp)
REVERT: C   64 MET cc_start: 0.1417 (mtt) cc_final: 0.0356 (mtt)
REVERT: C  138 ARG cc_start: 0.8079 (tmt170) cc_final: 0.7873 (tpt90)
REVERT: C  142 TYR cc_start: 0.8315 (t80) cc_final: 0.7747 (t80)
REVERT: C  147 GLU cc_start: 0.9113 (mp0) cc_final: 0.8847 (mp0)
REVERT: C  153 LYS cc_start: 0.9549 (mmpt) cc_final: 0.9231 (mmmt)
REVERT: C  184 LEU cc_start: 0.9754 (tt) cc_final: 0.9438 (tp)
REVERT: C  192 ARG cc_start: 0.4013 (mtt-85) cc_final: 0.1896 (mtt-85)
REVERT: C  222 LEU cc_start: 0.9049 (mt) cc_final: 0.8819 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 184
  average time/residue: 0.3502
  time to fit residues: 86.2627
Evaluate side-chains
  146 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 118 optimal weight:   10.0000
   chunk 3 optimal weight:   30.0000
   chunk 139 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 162 optimal weight:    8.9990
   chunk 115 optimal weight:    0.9980
   chunk 103 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 144 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 GLN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 GLN
C 111 GLN
C 172 ASN
** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.073470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.055955 restraints weight = 105068.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.057274 restraints weight = 73230.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.058333 restraints weight = 56125.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.6058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13329  Z= 0.189
  Angle     :  0.865  14.564  18103  Z= 0.431
  Chirality :  0.050   0.344   1999
  Planarity :  0.008   0.133   2359
  Dihedral  :  8.619 171.048   1829
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 24.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 17.79 %
    Favored  : 82.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.95 %
    Twisted General : 0.52 %

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: -3.76 (0.20), residues: 1630
  helix: -1.62 (0.24), residues: 377
  sheet: -1.99 (0.38), residues: 188
  loop : -3.13 (0.18), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 168 
 HIS   0.016   0.002   HIS A 375 
 PHE   0.044   0.002   PHE B  55 
 TYR   0.024   0.002   TYR C 346 
 ARG   0.011   0.001   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  262)
  hydrogen bonds       : angle       6.43709 (  696)
  covalent geometry    : bond        0.00415 (13327)
  covalent geometry    : angle       0.86540 (18103)
  Misc. bond           : bond        0.00353 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.460 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.8716 (m90) cc_final: 0.8407 (m-70)
REVERT: A   50 PHE cc_start: 0.9532 (m-80) cc_final: 0.9082 (m-80)
REVERT: A   57 MET cc_start: 0.9098 (mmm) cc_final: 0.8542 (mmm)
REVERT: A  258 LEU cc_start: 0.7461 (pt) cc_final: 0.7206 (pp)
REVERT: A  332 TYR cc_start: 0.7343 (m-80) cc_final: 0.7135 (m-80)
REVERT: A  364 MET cc_start: 0.7886 (tmm) cc_final: 0.6835 (ppp)
REVERT: A  385 MET cc_start: 0.5313 (ttm) cc_final: 0.5112 (ttm)
REVERT: A  402 MET cc_start: 0.9115 (mtm) cc_final: 0.8493 (mtm)
REVERT: A  530 LEU cc_start: 0.8905 (tp) cc_final: 0.8658 (tt)
REVERT: A  542 HIS cc_start: 0.8309 (m90) cc_final: 0.7831 (m170)
REVERT: A  580 ASN cc_start: 0.9244 (p0) cc_final: 0.8755 (p0)
REVERT: A  582 ASN cc_start: 0.8176 (m110) cc_final: 0.7508 (m110)
REVERT: A  584 ARG cc_start: 0.7295 (mmp-170) cc_final: 0.6992 (mmp-170)
REVERT: B   13 MET cc_start: 0.8942 (ttp) cc_final: 0.8231 (tpp)
REVERT: B   27 HIS cc_start: 0.9075 (t70) cc_final: 0.8860 (t70)
REVERT: B   80 TRP cc_start: 0.8175 (t-100) cc_final: 0.7446 (t-100)
REVERT: B  102 MET cc_start: 0.8450 (mmp) cc_final: 0.7852 (ppp)
REVERT: B  397 TRP cc_start: 0.6821 (t-100) cc_final: 0.6609 (t-100)
REVERT: B  402 MET cc_start: 0.7845 (mmm) cc_final: 0.7068 (mmm)
REVERT: B  474 ASN cc_start: 0.8763 (p0) cc_final: 0.8378 (p0)
REVERT: B  475 MET cc_start: 0.4973 (mtp) cc_final: 0.4288 (mtp)
REVERT: B  485 THR cc_start: 0.8875 (p) cc_final: 0.8672 (p)
REVERT: B  547 MET cc_start: 0.8919 (ptp) cc_final: 0.7906 (ptp)
REVERT: C  153 LYS cc_start: 0.9448 (mmpt) cc_final: 0.9112 (mmmt)
REVERT: C  192 ARG cc_start: 0.4289 (mtt-85) cc_final: 0.2095 (mtt-85)
REVERT: C  222 LEU cc_start: 0.8922 (mt) cc_final: 0.8635 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.3356
  time to fit residues: 78.0412
Evaluate side-chains
  146 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 42 optimal weight:    0.0570
   chunk 143 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.9102

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

Flipped N/Q/H residues before XYZ refinement:
A 360 HIS
A 375 HIS
A 569 GLN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 HIS
C 132 GLN
C 172 ASN
C 328 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.075343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.059264 restraints weight = 106820.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.060651 restraints weight = 73501.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.061692 restraints weight = 55589.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.6295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13329  Z= 0.137
  Angle     :  0.826  15.683  18103  Z= 0.411
  Chirality :  0.049   0.289   1999
  Planarity :  0.007   0.133   2359
  Dihedral  :  8.380 171.004   1829
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 15.89 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.95 %
    Twisted General : 0.46 %

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: -3.79 (0.19), residues: 1630
  helix: -1.58 (0.24), residues: 392
  sheet: -2.07 (0.38), residues: 175
  loop : -3.18 (0.18), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C  49 
 HIS   0.011   0.001   HIS A 375 
 PHE   0.046   0.002   PHE B  55 
 TYR   0.022   0.002   TYR C 346 
 ARG   0.011   0.001   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  262)
  hydrogen bonds       : angle       6.23937 (  696)
  covalent geometry    : bond        0.00306 (13327)
  covalent geometry    : angle       0.82603 (18103)
  Misc. bond           : bond        0.01121 (    2)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.841 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.8647 (m90) cc_final: 0.8352 (m-70)
REVERT: A   50 PHE cc_start: 0.9496 (m-80) cc_final: 0.9151 (m-80)
REVERT: A   57 MET cc_start: 0.9041 (mmm) cc_final: 0.8629 (mmm)
REVERT: A  332 TYR cc_start: 0.7293 (m-80) cc_final: 0.7062 (m-80)
REVERT: A  385 MET cc_start: 0.5429 (ttm) cc_final: 0.4327 (ttm)
REVERT: A  402 MET cc_start: 0.9092 (mtm) cc_final: 0.8485 (mtm)
REVERT: A  515 PHE cc_start: 0.8325 (t80) cc_final: 0.8035 (t80)
REVERT: A  530 LEU cc_start: 0.8777 (tp) cc_final: 0.8517 (tt)
REVERT: A  542 HIS cc_start: 0.8398 (m90) cc_final: 0.7897 (m170)
REVERT: A  580 ASN cc_start: 0.9232 (p0) cc_final: 0.8772 (p0)
REVERT: A  582 ASN cc_start: 0.8119 (m110) cc_final: 0.7416 (m110)
REVERT: B   13 MET cc_start: 0.8970 (ttp) cc_final: 0.8351 (tpp)
REVERT: B   27 HIS cc_start: 0.9032 (t70) cc_final: 0.8810 (t70)
REVERT: B   80 TRP cc_start: 0.8036 (t-100) cc_final: 0.7292 (t-100)
REVERT: B  102 MET cc_start: 0.8681 (mmp) cc_final: 0.8063 (ppp)
REVERT: B  397 TRP cc_start: 0.6747 (t-100) cc_final: 0.6479 (t-100)
REVERT: B  402 MET cc_start: 0.7694 (mmm) cc_final: 0.7007 (mmm)
REVERT: B  474 ASN cc_start: 0.8695 (p0) cc_final: 0.8279 (p0)
REVERT: B  475 MET cc_start: 0.4902 (mtp) cc_final: 0.4310 (mtp)
REVERT: B  521 LEU cc_start: 0.7780 (mt) cc_final: 0.7537 (mp)
REVERT: B  547 MET cc_start: 0.8819 (ptp) cc_final: 0.7111 (mtm)
REVERT: C   64 MET cc_start: 0.1715 (mtt) cc_final: 0.0781 (mtt)
REVERT: C   91 MET cc_start: 0.4516 (ptp) cc_final: 0.2894 (mmt)
REVERT: C  101 PRO cc_start: 0.9069 (Cg_exo) cc_final: 0.8714 (Cg_endo)
REVERT: C  142 TYR cc_start: 0.8631 (t80) cc_final: 0.7844 (t80)
REVERT: C  147 GLU cc_start: 0.9101 (mp0) cc_final: 0.8795 (mp0)
REVERT: C  153 LYS cc_start: 0.9522 (mmpt) cc_final: 0.9213 (mmmt)
REVERT: C  184 LEU cc_start: 0.9767 (tt) cc_final: 0.9477 (tp)
REVERT: C  192 ARG cc_start: 0.3913 (mtt-85) cc_final: 0.1814 (mtt-85)
REVERT: C  222 LEU cc_start: 0.8829 (mt) cc_final: 0.8524 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.3337
  time to fit residues: 80.5761
Evaluate side-chains
  146 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 148 optimal weight:   30.0000
   chunk 33 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 127 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0170
   chunk 117 optimal weight:    5.9990
   chunk 136 optimal weight:    5.9990
   chunk 119 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0980
   chunk 95 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0670
   overall best weight:    1.3558

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

Flipped N/Q/H residues before XYZ refinement:
A 569 GLN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 328 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.076508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.060125 restraints weight = 106184.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.061571 restraints weight = 72946.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.062640 restraints weight = 55039.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.6566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13329  Z= 0.130
  Angle     :  0.820  15.191  18103  Z= 0.404
  Chirality :  0.048   0.253   1999
  Planarity :  0.007   0.129   2359
  Dihedral  :  8.211 171.765   1829
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 15.21 %
    Favored  : 84.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.95 %
    Twisted General : 0.59 %

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: -3.73 (0.19), residues: 1630
  helix: -1.58 (0.24), residues: 398
  sheet: -1.94 (0.38), residues: 175
  loop : -3.14 (0.18), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C  49 
 HIS   0.006   0.001   HIS B 467 
 PHE   0.047   0.002   PHE B  55 
 TYR   0.022   0.001   TYR A 321 
 ARG   0.013   0.001   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  262)
  hydrogen bonds       : angle       6.12920 (  696)
  covalent geometry    : bond        0.00286 (13327)
  covalent geometry    : angle       0.81999 (18103)
  Misc. bond           : bond        0.00809 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4555.89 seconds
wall clock time: 79 minutes 37.07 seconds (4777.07 seconds total)