Starting phenix.real_space_refine
on Thu Mar 13 02:35:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jt2_9885/03_2025/6jt2_9885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jt2_9885/03_2025/6jt2_9885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jt2_9885/03_2025/6jt2_9885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jt2_9885/03_2025/6jt2_9885.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jt2_9885/03_2025/6jt2_9885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jt2_9885/03_2025/6jt2_9885.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P       3      5.49       5
     Mg      2      5.21       5
     S      56      5.16       5
     C    5262      2.51       5
     N    1392      2.21       5
     O    1475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8191
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3742
          Classifications: {'peptide': 506}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 23, 'TRANS': 482}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 261
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 216
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 162
    Chain: "B"
      Number of atoms: 4372
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 138
      Conformer: "B"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 138
          bond proxies already assigned to first conformer: 4452
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {' MG': 2, 'G2P': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU A 254 " occ=0.92
      ... (3 atoms not shown)
      pdb=" CB  LEU A 254 " occ=0.92
  Time building chain proxies: 7.15, per 1000 atoms: 0.87
  Number of scatterers: 8191
  At special positions: 0
  Unit cell: (147.345, 87.78, 98.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      1     26.01
     S      56     16.00
     P       3     15.00
     Mg      2     11.99
     O    1475      8.00
     N    1392      7.00
     C    5262      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 8 sheets defined
      50.4% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 128 through 149
      removed outlier: 3.585A  pdb=" N   ILE A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 4.375A  pdb=" N   VAL A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   VAL A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 150 through 155'
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.800A  pdb=" N   PHE A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 226
      removed outlier: 4.660A  pdb=" N   LEU A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ILE A 214 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      Proline residue:  A 216  - end of helix
      removed outlier: 3.643A  pdb=" N   LYS A 220 " --> pdb=" O   PRO A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 302 through 309
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 408 through 458
      removed outlier: 4.206A  pdb=" N   VAL A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 4.336A  pdb=" N   GLN A 468 " --> pdb=" O   GLN A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 497
      removed outlier: 3.508A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.517A  pdb=" N   GLN A 516 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU A 519 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 561
      removed outlier: 3.649A  pdb=" N   GLN A 548 " --> pdb=" O   THR A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
      removed outlier: 3.642A  pdb=" N   ASN A 605 " --> pdb=" O   VAL A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 628
      removed outlier: 4.133A  pdb=" N   ASP A 628 " --> pdb=" O   ARG A 624 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 4.201A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 30
      removed outlier: 3.931A  pdb=" N   TRP B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.803A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 82
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.938A  pdb=" N   LEU B  87 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU B  90 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 112
      removed outlier: 4.732A  pdb=" N   ASP B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ALA B 103 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
      removed outlier: 4.206A  pdb=" N   ILE B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 249 through 253
      removed outlier: 3.692A  pdb=" N   VAL B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 253'
    Processing helix  chain 'B' and resid 264 through 271
      removed outlier: 3.892A  pdb=" N   SER B 270 " --> pdb=" O   HIS B 266 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   HIS B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 285
      removed outlier: 4.350A  pdb=" N   LEU B 285 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 282 through 285'
    Processing helix  chain 'B' and resid 329 through 335
      removed outlier: 3.575A  pdb=" N   LEU B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 348 through 398
      removed outlier: 4.370A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 408
      removed outlier: 4.384A  pdb=" N   HIS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
    Processing helix  chain 'B' and resid 443 through 461
    Processing helix  chain 'B' and resid 491 through 507
      removed outlier: 3.532A  pdb=" N   SER B 495 " --> pdb=" O   HIS B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.641A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 573
    Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 204
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300
      removed outlier: 6.563A  pdb=" N   MET A 291 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525
      removed outlier: 4.409A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   MET A 573 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   ASN A 617 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE A 575 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ILE A 616 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 124
    Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.692A  pdb=" N   GLN B 231 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL B 277 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 415 through 416
      removed outlier: 3.532A  pdb=" N   GLY B 531 " --> pdb=" O   CYS B 541 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 469 through 474
      removed outlier: 7.068A  pdb=" N   MET B 480 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   THR B 474 " --> pdb=" O   LYS B 478 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LYS B 478 " --> pdb=" O   THR B 474 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR B 421 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   SER B 565 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ILE B 523 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ILE B 562 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLY B 588 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   PHE B 603 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   HIS B 586 " --> pdb=" O   PHE B 603 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER B 605 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   LEU B 584 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512

    461 hydrogen bonds defined for protein.
    1326 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: 2.71

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 3335
        1.39 -     1.56: 4924
        1.56 -     1.73: 6
        1.73 -     1.90: 86
        1.90 -     2.07: 4
  Bond restraints: 8355
  Sorted by residual:
  bond pdb=" O3B G2P A1001 "
       pdb=" PG  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.716  1.610  0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" O1A G2P A1001 "
       pdb=" PA  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.507  1.610 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" O1B G2P A1001 "
       pdb=" PB  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.510  1.609 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C4  G2P A1001 "
       pdb=" C5  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.384  1.469 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C5  G2P A1001 "
       pdb=" C6  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.420  1.483 -0.063 2.00e-02 2.50e+03 9.79e+00
  ... (remaining 8350 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 11160
        2.27 -     4.54: 170
        4.54 -     6.81: 22
        6.81 -     9.09: 11
        9.09 -    11.36: 4
  Bond angle restraints: 11367
  Sorted by residual:
  angle pdb=" PA  G2P A1001 "
        pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     120.83  109.47   11.36 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
        pdb=" O3B G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.71  109.82  -10.11 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" C5  G2P A1001 "
        pdb=" C4  G2P A1001 "
        pdb=" N3  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     128.08  118.69    9.39 3.00e+00 1.11e-01 9.79e+00
  angle pdb=" C   TYR B 339 "
        pdb=" N   LEU B 340 "
        pdb=" CA  LEU B 340 "
      ideal   model   delta    sigma   weight residual
     121.54  127.36   -5.82 1.91e+00 2.74e-01 9.28e+00
  angle pdb=" C3A G2P A1001 "
        pdb=" PA  G2P A1001 "
        pdb=" O5' G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.14  108.27   -9.13 3.00e+00 1.11e-01 9.26e+00
  ... (remaining 11362 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 4668
       16.26 -    32.52: 249
       32.52 -    48.78: 56
       48.78 -    65.03: 15
       65.03 -    81.29: 4
  Dihedral angle restraints: 4992
    sinusoidal: 1869
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" CA  ASP B 262 "
           pdb=" C   ASP B 262 "
           pdb=" N   ILE B 263 "
           pdb=" CA  ILE B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.33  -24.67     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  TYR B 339 "
           pdb=" C   TYR B 339 "
           pdb=" N   LEU B 340 "
           pdb=" CA  LEU B 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.25  -21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  PHE A 301 "
           pdb=" C   PHE A 301 "
           pdb=" N   GLY A 302 "
           pdb=" CA  GLY A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1106
       0.055 -    0.111: 213
       0.111 -    0.166: 22
       0.166 -    0.221: 0
       0.221 -    0.276: 1
  Chirality restraints: 1342
  Sorted by residual:
  chirality pdb=" CB  VAL A 462 "
            pdb=" CA  VAL A 462 "
            pdb=" CG1 VAL A 462 "
            pdb=" CG2 VAL A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  VAL A 462 "
            pdb=" N   VAL A 462 "
            pdb=" C   VAL A 462 "
            pdb=" CB  VAL A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.18e-01
  chirality pdb=" C2' G2P A1001 "
            pdb=" C1' G2P A1001 "
            pdb=" C3' G2P A1001 "
            pdb=" O2' G2P A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.62    0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 1339 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 462 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" C   VAL A 462 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL A 462 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA A 463 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 258 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.31e+00
        pdb=" N   PRO B 259 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 209 "    0.037 5.00e-02 4.00e+02   5.67e-02 5.14e+00
        pdb=" N   PRO B 210 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 210 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 210 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 47
        2.56 -     3.15: 6531
        3.15 -     3.73: 12626
        3.73 -     4.32: 16476
        4.32 -     4.90: 27806
  Nonbonded interactions: 63486
  Sorted by model distance:
  nonbonded pdb=" O2B G2P A1001 "
            pdb="MG    MG A1002 "
     model   vdw
     1.980 2.170
  nonbonded pdb=" OD1 ASP A 486 "
            pdb="MG    MG A1002 "
     model   vdw
     2.095 2.170
  nonbonded pdb=" OD2 ASP A 486 "
            pdb="MG    MG A1002 "
     model   vdw
     2.101 2.170
  nonbonded pdb=" O5' G2P A1001 "
            pdb="MG    MG A1003 "
     model   vdw
     2.172 2.170
  nonbonded pdb=" O   LEU A 520 "
            pdb=" NE2 GLN A 548 "
     model   vdw
     2.259 3.120
  ... (remaining 63481 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 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:             0.880
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.020
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   8355  Z= 0.283
  Angle     :  0.738  11.357  11367  Z= 0.377
  Chirality :  0.042   0.276   1342
  Planarity :  0.005   0.058   1431
  Dihedral  : 11.363  81.292   2966
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.00 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  5.19 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.23), residues: 1049
  helix: -1.24 (0.20), residues: 478
  sheet: -1.17 (0.35), residues: 192
  loop : -2.34 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 602 
 HIS   0.005   0.001   HIS B 105 
 PHE   0.016   0.002   PHE A 292 
 TYR   0.013   0.001   TYR B 479 
 ARG   0.003   0.000   ARG B 552 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 CYS cc_start: 0.8998 (t) cc_final: 0.8778 (m)
REVERT: A  455 CYS cc_start: 0.8971 (m) cc_final: 0.8406 (t)
REVERT: A  479 ASN cc_start: 0.7920 (m110) cc_final: 0.7647 (p0)
REVERT: A  514 ASP cc_start: 0.9019 (m-30) cc_final: 0.8740 (m-30)
REVERT: A  516 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8498 (mm-40)
REVERT: A  543 ASP cc_start: 0.8435 (m-30) cc_final: 0.7491 (p0)
REVERT: A  554 VAL cc_start: 0.9375 (t) cc_final: 0.9168 (t)
REVERT: A  556 MET cc_start: 0.9443 (tpp) cc_final: 0.8926 (mmm)
REVERT: A  583 PHE cc_start: 0.8186 (m-80) cc_final: 0.7859 (m-10)
REVERT: B   73 MET cc_start: 0.8564 (tpp) cc_final: 0.8300 (tpp)
REVERT: B  106 ASP cc_start: 0.9202 (t0) cc_final: 0.8917 (t0)
REVERT: B  119 SER cc_start: 0.9177 (m) cc_final: 0.8363 (p)
REVERT: B  160 THR cc_start: 0.8562 (m) cc_final: 0.8351 (p)
REVERT: B  211 TYR cc_start: 0.8649 (t80) cc_final: 0.8372 (t80)
REVERT: B  228 VAL cc_start: 0.8802 (t) cc_final: 0.8571 (p)
REVERT: B  320 LEU cc_start: 0.8545 (tt) cc_final: 0.8089 (tp)
REVERT: B  323 CYS cc_start: 0.8540 (p) cc_final: 0.8244 (p)
REVERT: B  394 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8711 (tt)
REVERT: B  491 HIS cc_start: 0.8482 (p90) cc_final: 0.7513 (t-170)
REVERT: B  537 MET cc_start: 0.8659 (ttm) cc_final: 0.8425 (ttt)
  outliers start: 30
  outliers final: 11
  residues processed: 212
  average time/residue: 0.2183
  time to fit residues: 63.6523
Evaluate side-chains
  123 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  260 HIS
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   chunk 96 optimal weight:   10.0000
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
B 408 HIS
B 548 ASN
B 563 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.107857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.086558 restraints weight = 25653.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.087368 restraints weight = 15965.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.088352 restraints weight = 12850.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8355  Z= 0.205
  Angle     :  0.695  10.250  11367  Z= 0.348
  Chirality :  0.043   0.191   1342
  Planarity :  0.005   0.047   1431
  Dihedral  :  7.828  69.584   1203
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 12.63 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1049
  helix:  0.43 (0.22), residues: 487
  sheet: -0.91 (0.35), residues: 207
  loop : -2.00 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP A 467 
 HIS   0.010   0.001   HIS B 266 
 PHE   0.024   0.002   PHE A 335 
 TYR   0.025   0.002   TYR B 237 
 ARG   0.008   0.001   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6448 (t80)
REVERT: A  455 CYS cc_start: 0.7747 (m) cc_final: 0.7201 (t)
REVERT: A  511 THR cc_start: 0.9174 (p) cc_final: 0.8972 (t)
REVERT: A  543 ASP cc_start: 0.7731 (m-30) cc_final: 0.7101 (p0)
REVERT: A  583 PHE cc_start: 0.8134 (m-80) cc_final: 0.7926 (m-10)
REVERT: B  106 ASP cc_start: 0.8676 (t0) cc_final: 0.8270 (t0)
REVERT: B  119 SER cc_start: 0.8915 (m) cc_final: 0.7887 (p)
REVERT: B  491 HIS cc_start: 0.7410 (p90) cc_final: 0.7182 (t-170)
REVERT: B  537 MET cc_start: 0.8301 (ttm) cc_final: 0.8018 (ttt)
  outliers start: 34
  outliers final: 21
  residues processed: 144
  average time/residue: 0.1626
  time to fit residues: 34.7702
Evaluate side-chains
  124 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 4 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
B 266 HIS
B 408 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.077826 restraints weight = 19312.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.080048 restraints weight = 12481.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.081589 restraints weight = 9271.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.108   8355  Z= 0.441
  Angle     :  0.774   8.464  11367  Z= 0.393
  Chirality :  0.048   0.286   1342
  Planarity :  0.005   0.050   1431
  Dihedral  :  7.738  62.923   1198
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 14.40 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1049
  helix:  0.66 (0.23), residues: 494
  sheet: -0.82 (0.36), residues: 210
  loop : -1.86 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP B  22 
 HIS   0.009   0.002   HIS B 266 
 PHE   0.029   0.003   PHE A 458 
 TYR   0.019   0.002   TYR B 569 
 ARG   0.005   0.001   ARG B 121 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7147 (pp)
REVERT: A  203 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6463 (t80)
REVERT: A  399 TYR cc_start: 0.7189 (m-80) cc_final: 0.6852 (m-10)
REVERT: A  455 CYS cc_start: 0.7582 (m) cc_final: 0.7255 (t)
REVERT: A  556 MET cc_start: 0.9047 (mmm) cc_final: 0.8730 (tpp)
REVERT: B    9 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8282 (tt)
REVERT: B  106 ASP cc_start: 0.8670 (t0) cc_final: 0.8203 (t0)
REVERT: B  119 SER cc_start: 0.9187 (m) cc_final: 0.8371 (p)
REVERT: B  342 ASP cc_start: 0.7559 (m-30) cc_final: 0.7297 (m-30)
REVERT: B  491 HIS cc_start: 0.7518 (p90) cc_final: 0.7258 (t-170)
  outliers start: 39
  outliers final: 25
  residues processed: 135
  average time/residue: 0.1473
  time to fit residues: 30.1320
Evaluate side-chains
  111 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    0.0770
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0770
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0060
   chunk 66 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0170
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.1750

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
A 479 ASN
A 516 GLN
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.106192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.082279 restraints weight = 23342.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.085046 restraints weight = 13487.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.086968 restraints weight = 9323.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8355  Z= 0.157
  Angle     :  0.621   8.528  11367  Z= 0.308
  Chirality :  0.041   0.146   1342
  Planarity :  0.004   0.045   1431
  Dihedral  :  7.447  68.325   1198
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 15.58 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1049
  helix:  1.17 (0.23), residues: 491
  sheet: -0.49 (0.36), residues: 210
  loop : -1.77 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B  22 
 HIS   0.013   0.001   HIS B 498 
 PHE   0.017   0.002   PHE B 433 
 TYR   0.014   0.001   TYR B 237 
 ARG   0.005   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6746 (pp)
REVERT: A  203 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6490 (t80)
REVERT: A  471 VAL cc_start: 0.7873 (t) cc_final: 0.7643 (m)
REVERT: A  607 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7669 (t80)
REVERT: B   61 LEU cc_start: 0.8339 (pt) cc_final: 0.8032 (tt)
REVERT: B  106 ASP cc_start: 0.8598 (t0) cc_final: 0.8058 (t0)
REVERT: B  119 SER cc_start: 0.9129 (m) cc_final: 0.8237 (p)
REVERT: B  491 HIS cc_start: 0.7462 (p90) cc_final: 0.7183 (t-170)
REVERT: B  592 MET cc_start: 0.7503 (ppp) cc_final: 0.7252 (ppp)
  outliers start: 36
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1727
  time to fit residues: 35.1568
Evaluate side-chains
  118 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 49 optimal weight:    0.2980
   chunk 9 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0070
   overall best weight:    1.0604

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN
B 451 ASN
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.103800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.081090 restraints weight = 41470.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.082365 restraints weight = 26129.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.083145 restraints weight = 18606.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8355  Z= 0.227
  Angle     :  0.623   8.099  11367  Z= 0.308
  Chirality :  0.042   0.242   1342
  Planarity :  0.004   0.047   1431
  Dihedral  :  6.773  63.371   1196
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 16.17 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1049
  helix:  1.31 (0.23), residues: 492
  sheet: -0.34 (0.36), residues: 210
  loop : -1.70 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  22 
 HIS   0.010   0.001   HIS B 498 
 PHE   0.018   0.002   PHE B 433 
 TYR   0.011   0.001   TYR B 479 
 ARG   0.003   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6995 (pp)
REVERT: A  203 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6629 (t80)
REVERT: A  399 TYR cc_start: 0.7398 (m-80) cc_final: 0.7087 (m-80)
REVERT: A  471 VAL cc_start: 0.8074 (t) cc_final: 0.7872 (m)
REVERT: B   61 LEU cc_start: 0.8378 (pt) cc_final: 0.8095 (tt)
REVERT: B  106 ASP cc_start: 0.8691 (t0) cc_final: 0.8129 (t0)
  outliers start: 36
  outliers final: 26
  residues processed: 131
  average time/residue: 0.1999
  time to fit residues: 39.6957
Evaluate side-chains
  125 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0870
   chunk 104 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.105073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.082602 restraints weight = 34825.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.083755 restraints weight = 20782.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.084439 restraints weight = 18693.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8355  Z= 0.177
  Angle     :  0.601  10.652  11367  Z= 0.295
  Chirality :  0.041   0.210   1342
  Planarity :  0.004   0.045   1431
  Dihedral  :  6.551  64.685   1196
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 16.65 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.26), residues: 1049
  helix:  1.48 (0.23), residues: 489
  sheet: -0.13 (0.36), residues: 210
  loop : -1.63 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  22 
 HIS   0.011   0.001   HIS B 498 
 PHE   0.013   0.001   PHE A 458 
 TYR   0.012   0.001   TYR B 479 
 ARG   0.004   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6654 (t80)
REVERT: A  399 TYR cc_start: 0.7382 (m-80) cc_final: 0.7061 (m-80)
REVERT: A  607 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7613 (t80)
REVERT: B   61 LEU cc_start: 0.8378 (pt) cc_final: 0.8117 (tt)
REVERT: B  106 ASP cc_start: 0.8708 (t0) cc_final: 0.8098 (t0)
  outliers start: 37
  outliers final: 22
  residues processed: 130
  average time/residue: 0.1501
  time to fit residues: 29.7254
Evaluate side-chains
  115 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 87 optimal weight:    0.4980
   chunk 10 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 419 ASN
B 563 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.104422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.081483 restraints weight = 18823.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.083772 restraints weight = 11958.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.085385 restraints weight = 8803.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8355  Z= 0.193
  Angle     :  0.610  10.123  11367  Z= 0.298
  Chirality :  0.041   0.236   1342
  Planarity :  0.004   0.046   1431
  Dihedral  :  6.371  63.195   1193
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.12 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1049
  helix:  1.47 (0.23), residues: 490
  sheet: -0.09 (0.37), residues: 210
  loop : -1.56 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  22 
 HIS   0.009   0.001   HIS B 266 
 PHE   0.016   0.002   PHE B 321 
 TYR   0.012   0.001   TYR B 479 
 ARG   0.003   0.000   ARG B 238 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6570 (t80)
REVERT: A  399 TYR cc_start: 0.7325 (m-80) cc_final: 0.7048 (m-80)
REVERT: A  607 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7614 (t80)
REVERT: B   61 LEU cc_start: 0.8311 (pt) cc_final: 0.8100 (tt)
  outliers start: 34
  outliers final: 27
  residues processed: 125
  average time/residue: 0.1509
  time to fit residues: 28.7665
Evaluate side-chains
  119 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 102 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0070
   chunk 49 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 79 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.8200

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 491 HIS
B 563 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.105353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.082847 restraints weight = 31797.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.084515 restraints weight = 18928.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.085377 restraints weight = 13401.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8355  Z= 0.195
  Angle     :  0.620  11.260  11367  Z= 0.301
  Chirality :  0.041   0.219   1342
  Planarity :  0.004   0.047   1431
  Dihedral  :  6.374  62.641   1193
  Min Nonbonded Distance : 1.665

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.24 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1049
  helix:  1.45 (0.23), residues: 494
  sheet: -0.01 (0.37), residues: 208
  loop : -1.49 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  22 
 HIS   0.015   0.001   HIS B 266 
 PHE   0.015   0.002   PHE B 321 
 TYR   0.014   0.001   TYR A 372 
 ARG   0.003   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6623 (t80)
REVERT: A  399 TYR cc_start: 0.7448 (m-80) cc_final: 0.7084 (m-80)
REVERT: A  607 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7643 (t80)
REVERT: B   61 LEU cc_start: 0.8367 (pt) cc_final: 0.8133 (tt)
REVERT: B  503 MET cc_start: 0.8757 (mmm) cc_final: 0.8477 (mmm)
  outliers start: 31
  outliers final: 25
  residues processed: 120
  average time/residue: 0.1951
  time to fit residues: 36.2311
Evaluate side-chains
  117 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0060
   chunk 53 optimal weight:    3.9990
   chunk 105 optimal weight:    7.9990
   overall best weight:    1.3600

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 491 HIS
B 563 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.103096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.080229 restraints weight = 32094.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.082287 restraints weight = 19084.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.082772 restraints weight = 14584.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8355  Z= 0.256
  Angle     :  0.645  11.560  11367  Z= 0.316
  Chirality :  0.042   0.204   1342
  Planarity :  0.004   0.048   1431
  Dihedral  :  6.414  58.091   1193
  Min Nonbonded Distance : 1.412

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 16.77 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 1049
  helix:  1.42 (0.23), residues: 493
  sheet:  0.10 (0.38), residues: 208
  loop : -1.46 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  22 
 HIS   0.015   0.002   HIS B 266 
 PHE   0.015   0.002   PHE B 321 
 TYR   0.012   0.001   TYR A 372 
 ARG   0.003   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 84
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6630 (t80)
REVERT: A  607 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7888 (t80)
REVERT: B   61 LEU cc_start: 0.8429 (pt) cc_final: 0.8170 (tt)
REVERT: B   65 GLU cc_start: 0.7725 (tp30) cc_final: 0.7427 (tp30)
REVERT: B  503 MET cc_start: 0.8826 (mmm) cc_final: 0.8522 (mmm)
  outliers start: 35
  outliers final: 29
  residues processed: 114
  average time/residue: 0.1551
  time to fit residues: 26.7743
Evaluate side-chains
  114 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0060
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0670
   chunk 97 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0770
   overall best weight:    0.1670

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.106107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.084941 restraints weight = 22035.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.084626 restraints weight = 14276.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.085130 restraints weight = 12240.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.4487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8355  Z= 0.153
  Angle     :  0.625  12.553  11367  Z= 0.300
  Chirality :  0.041   0.261   1342
  Planarity :  0.004   0.051   1431
  Dihedral  :  6.395  63.668   1193
  Min Nonbonded Distance : 1.472

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.71 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 1049
  helix:  1.55 (0.24), residues: 494
  sheet:  0.16 (0.38), residues: 208
  loop : -1.42 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  22 
 HIS   0.015   0.001   HIS B 266 
 PHE   0.016   0.002   PHE B 321 
 TYR   0.015   0.001   TYR A 372 
 ARG   0.003   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6592 (t80)
REVERT: A  607 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7617 (t80)
REVERT: A  626 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8114 (mm)
REVERT: B   61 LEU cc_start: 0.8354 (pt) cc_final: 0.8153 (tt)
REVERT: B  334 THR cc_start: 0.9082 (m) cc_final: 0.8867 (p)
REVERT: B  503 MET cc_start: 0.8835 (mmm) cc_final: 0.8545 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 117
  average time/residue: 0.1490
  time to fit residues: 26.3159
Evaluate side-chains
  114 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.0570
   chunk 96 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 105 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.9702

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.104731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.082756 restraints weight = 22542.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.083488 restraints weight = 13685.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.084292 restraints weight = 11855.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8355  Z= 0.212
  Angle     :  0.628  12.474  11367  Z= 0.304
  Chirality :  0.042   0.281   1342
  Planarity :  0.004   0.052   1431
  Dihedral  :  6.285  60.581   1193
  Min Nonbonded Distance : 1.362

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 18.06 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.27), residues: 1049
  helix:  1.59 (0.24), residues: 494
  sheet:  0.23 (0.38), residues: 208
  loop : -1.41 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  22 
 HIS   0.009   0.001   HIS B 498 
 PHE   0.015   0.002   PHE B 321 
 TYR   0.012   0.001   TYR A 372 
 ARG   0.003   0.000   ARG B 381 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2982.73 seconds
wall clock time: 54 minutes 37.97 seconds (3277.97 seconds total)