Starting phenix.real_space_refine
on Wed Mar 12 11:20:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t4e_41028/03_2025/8t4e_41028.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4e_41028/03_2025/8t4e_41028.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t4e_41028/03_2025/8t4e_41028.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4e_41028/03_2025/8t4e_41028.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4e_41028/03_2025/8t4e_41028.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4e_41028/03_2025/8t4e_41028.cif"
  }
  resolution = 3.5
  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=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4886      2.51       5
     N    1356      2.21       5
     O    1441      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 7714
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 3417
          Classifications: {'peptide': 529}
          Incomplete info: {'truncation_to_alanine': 190}
          Link IDs: {'PTRANS': 18, 'TRANS': 510}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 683
          Unresolved non-hydrogen angles: 881
          Unresolved non-hydrogen dihedrals: 545
          Unresolved non-hydrogen chiralities: 75
          Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 16, 'HIS:plan': 7}
          Unresolved non-hydrogen planarities: 400
    Chain: "B"
      Number of atoms: 4227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4227
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 20, 'TRANS': 530}
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 62
    Chain: "C"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 70
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
  Time building chain proxies: 5.37, per 1000 atoms: 0.70
  Number of scatterers: 7714
  At special positions: 0
  Unit cell: (73.832, 104.875, 134.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1441      8.00
     N    1356      7.00
     C    4886      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: 1.68
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2008

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      71.9% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 183 through 202
      removed outlier: 3.993A  pdb=" N   MET A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 217
      removed outlier: 4.007A  pdb=" N   PHE A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 270
      removed outlier: 3.587A  pdb=" N   HIS A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG A 270 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 324
    Processing helix  chain 'A' and resid 324 through 373
      removed outlier: 3.504A  pdb=" N   THR A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
      removed outlier: 5.569A  pdb=" N   LEU A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      Proline residue:  A 342  - end of helix
      removed outlier: 3.831A  pdb=" N   LYS A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 382 through 437
      removed outlier: 4.266A  pdb=" N   THR A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   GLY A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 476
      removed outlier: 3.905A  pdb=" N   MET A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      Proline residue:  A 466  - end of helix
    Processing helix  chain 'A' and resid 539 through 542
    Processing helix  chain 'A' and resid 543 through 552
    Processing helix  chain 'A' and resid 573 through 581
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 628
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.563A  pdb=" N   THR A 634 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 644 through 658
    Processing helix  chain 'A' and resid 674 through 686
    Processing helix  chain 'A' and resid 688 through 694
      removed outlier: 3.537A  pdb=" N   ARG A 691 " --> pdb=" O   SER A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 708
      removed outlier: 3.873A  pdb=" N   VAL A 706 " --> pdb=" O   HIS A 702 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 707 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLN A 708 " --> pdb=" O   SER A 704 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 702 through 708'
    Processing helix  chain 'A' and resid 725 through 732
    Processing helix  chain 'A' and resid 734 through 742
    Processing helix  chain 'B' and resid 132 through 146
    Processing helix  chain 'B' and resid 148 through 182
      Proline residue:  B 170  - end of helix
      removed outlier: 3.837A  pdb=" N   ILE B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLY B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 234
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.662A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 255
      removed outlier: 3.688A  pdb=" N   LEU B 249 " --> pdb=" O   LYS B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 260
      removed outlier: 3.746A  pdb=" N   MET B 260 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 263
      No H-bonds generated for 'chain 'B' and resid 261 through 263'
    Processing helix  chain 'B' and resid 266 through 289
    Processing helix  chain 'B' and resid 289 through 338
      removed outlier: 4.189A  pdb=" N   LEU B 295 " --> pdb=" O   ARG B 291 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      Proline residue:  B 301  - end of helix
      removed outlier: 3.652A  pdb=" N   VAL B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
    Processing helix  chain 'B' and resid 347 through 400
      removed outlier: 3.612A  pdb=" N   LEU B 365 " --> pdb=" O   GLN B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 448
      removed outlier: 3.684A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   GLN B 424 " --> pdb=" O   GLY B 420 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 516
      removed outlier: 3.715A  pdb=" N   ALA B 513 " --> pdb=" O   LYS B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 537
      No H-bonds generated for 'chain 'B' and resid 535 through 537'
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 572 through 583
      removed outlier: 3.566A  pdb=" N   VAL B 576 " --> pdb=" O   GLU B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 592
      removed outlier: 3.831A  pdb=" N   GLU B 591 " --> pdb=" O   ASP B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 598
      removed outlier: 3.737A  pdb=" N   THR B 598 " --> pdb=" O   GLY B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 622
    Processing helix  chain 'B' and resid 638 through 646
    Processing helix  chain 'B' and resid 647 through 652
      removed outlier: 6.691A  pdb=" N   SER B 650 " --> pdb=" O   ASP B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 668
    Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528
      removed outlier: 3.819A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 511
      removed outlier: 7.274A  pdb=" N   PHE A 510 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   GLN A 522 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 534 through 537
      removed outlier: 6.463A  pdb=" N   PHE A 714 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 664
    Processing sheet with id=AA5, first strand: chain 'B' and resid 489 through 493
      removed outlier: 4.763A  pdb=" N   LEU B 489 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE B 491 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL B 468 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   PHE B 470 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   LEU B 528 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   ASP B 472 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   GLN B 526 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 549
      removed outlier: 6.486A  pdb=" N   VAL B 498 " --> pdb=" O   GLN B 671 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   LEU B 673 " --> pdb=" O   VAL B 498 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   LEU B 675 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   VAL B 502 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)

    599 hydrogen bonds defined for protein.
    1740 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: 2.53

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2612
        1.34 -     1.46: 1673
        1.46 -     1.58: 3501
        1.58 -     1.70: 0
        1.70 -     1.82: 53
  Bond restraints: 7839
  Sorted by residual:
  bond pdb=" CA  GLN B 471 "
       pdb=" C   GLN B 471 "
    ideal  model  delta    sigma   weight residual
    1.526  1.496  0.030 1.30e-02 5.92e+03 5.32e+00
  bond pdb=" CA  SER B 474 "
       pdb=" C   SER B 474 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 1.20e-02 6.94e+03 4.57e+00
  bond pdb=" N   VAL B 473 "
       pdb=" CA  VAL B 473 "
    ideal  model  delta    sigma   weight residual
    1.457  1.438  0.019 1.19e-02 7.06e+03 2.57e+00
  bond pdb=" CA  VAL B 473 "
       pdb=" C   VAL B 473 "
    ideal  model  delta    sigma   weight residual
    1.522  1.501  0.021 1.35e-02 5.49e+03 2.43e+00
  bond pdb=" CA  LYS B 469 "
       pdb=" C   LYS B 469 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.018 1.24e-02 6.50e+03 2.21e+00
  ... (remaining 7834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 10486
        1.99 -     3.99: 145
        3.99 -     5.98: 32
        5.98 -     7.98: 12
        7.98 -     9.97: 5
  Bond angle restraints: 10680
  Sorted by residual:
  angle pdb=" CA  TRP A 348 "
        pdb=" CB  TRP A 348 "
        pdb=" CG  TRP A 348 "
      ideal   model   delta    sigma   weight residual
     113.60  120.43   -6.83 1.90e+00 2.77e-01 1.29e+01
  angle pdb=" CA  LYS C   3 "
        pdb=" CB  LYS C   3 "
        pdb=" CG  LYS C   3 "
      ideal   model   delta    sigma   weight residual
     114.10  120.86   -6.76 2.00e+00 2.50e-01 1.14e+01
  angle pdb=" CG  ARG A 357 "
        pdb=" CD  ARG A 357 "
        pdb=" NE  ARG A 357 "
      ideal   model   delta    sigma   weight residual
     112.00  119.28   -7.28 2.20e+00 2.07e-01 1.10e+01
  angle pdb=" CB  MET A 420 "
        pdb=" CG  MET A 420 "
        pdb=" SD  MET A 420 "
      ideal   model   delta    sigma   weight residual
     112.70  122.52   -9.82 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" C   ASP B 472 "
        pdb=" N   VAL B 473 "
        pdb=" CA  VAL B 473 "
      ideal   model   delta    sigma   weight residual
     120.50  116.13    4.37 1.34e+00 5.57e-01 1.06e+01
  ... (remaining 10675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4135
       17.98 -    35.97: 406
       35.97 -    53.95: 113
       53.95 -    71.94: 17
       71.94 -    89.92: 9
  Dihedral angle restraints: 4680
    sinusoidal: 1563
      harmonic: 3117
  Sorted by residual:
  dihedral pdb=" CA  ILE A 397 "
           pdb=" C   ILE A 397 "
           pdb=" N   LYS A 398 "
           pdb=" CA  LYS A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CB  GLU B 227 "
           pdb=" CG  GLU B 227 "
           pdb=" CD  GLU B 227 "
           pdb=" OE1 GLU B 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.92   89.92     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  GLU B 166 "
           pdb=" CG  GLU B 166 "
           pdb=" CD  GLU B 166 "
           pdb=" OE1 GLU B 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.38  -89.38     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 4677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 788
       0.028 -    0.056: 294
       0.056 -    0.084: 118
       0.084 -    0.111: 60
       0.111 -    0.139: 20
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CA  MET B 300 "
            pdb=" N   MET B 300 "
            pdb=" C   MET B 300 "
            pdb=" CB  MET B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  MET B 592 "
            pdb=" N   MET B 592 "
            pdb=" C   MET B 592 "
            pdb=" CB  MET B 592 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  PHE B 470 "
            pdb=" N   PHE B 470 "
            pdb=" C   PHE B 470 "
            pdb=" CB  PHE B 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1277 not shown)

  Planarity restraints: 1395
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 341 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+00
        pdb=" N   PRO A 342 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 342 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 342 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 428 "    0.008 2.00e-02 2.50e+03   1.22e-02 2.97e+00
        pdb=" CG  TYR B 428 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 428 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 428 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 428 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 428 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 428 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 428 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 460 "    0.025 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO B 461 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 461 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 461 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1392 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2159
        2.81 -     3.33: 7661
        3.33 -     3.85: 12709
        3.85 -     4.38: 12757
        4.38 -     4.90: 23342
  Nonbonded interactions: 58628
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 353 "
            pdb=" NE  ARG A 357 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   THR A 292 "
            pdb=" OG  SER A 296 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" NH2 ARG B 561 "
            pdb=" O   CYS B 571 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" OE1 GLU B 307 "
            pdb=" OH  TYR B 376 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OG  SER B 296 "
            pdb=" OE1 GLN B 416 "
     model   vdw
     2.357 3.040
  ... (remaining 58623 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.580
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.050
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
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      :  0.003   0.043   7839  Z= 0.208
  Angle     :  0.655   9.970  10680  Z= 0.342
  Chirality :  0.040   0.139   1280
  Planarity :  0.004   0.047   1395
  Dihedral  : 16.232  89.924   2672
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 26.38 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.25), residues: 1079
  helix:  2.04 (0.18), residues: 720
  sheet: -0.73 (0.74), residues: 51
  loop : -0.45 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 214 
 HIS   0.003   0.001   HIS B 543 
 PHE   0.020   0.002   PHE B 157 
 TYR   0.029   0.001   TYR B 428 
 ARG   0.011   0.000   ARG A 357 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  290 GLU cc_start: 0.6812 (pm20) cc_final: 0.6589 (pm20)
REVERT: A  329 MET cc_start: 0.6811 (tpt) cc_final: 0.6551 (mmt)
REVERT: A  347 LYS cc_start: 0.8261 (mttt) cc_final: 0.7753 (pptt)
REVERT: A  420 MET cc_start: 0.7087 (mmp) cc_final: 0.6474 (mmt)
REVERT: B  195 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6109 (t80)
REVERT: B  227 GLU cc_start: 0.6870 (tp30) cc_final: 0.6667 (tt0)
REVERT: B  245 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7539 (mmtm)
REVERT: B  256 ASP cc_start: 0.8068 (t0) cc_final: 0.7656 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2339
  time to fit residues: 39.3915
Evaluate side-chains
  96 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 83 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0970
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 518 ASN
B 539 HIS
** B 613 GLN ** 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 = 0.4157 r_free = 0.4157 target = 0.173328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.146537 restraints weight = 9858.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.145498 restraints weight = 7688.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146041 restraints weight = 6670.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7839  Z= 0.183
  Angle     :  0.488   7.839  10680  Z= 0.252
  Chirality :  0.037   0.130   1280
  Planarity :  0.003   0.042   1395
  Dihedral  :  3.522  54.982   1155
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 27.36 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.26), residues: 1079
  helix:  2.65 (0.18), residues: 724
  sheet: -0.54 (0.78), residues: 51
  loop : -0.24 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 214 
 HIS   0.004   0.001   HIS B 584 
 PHE   0.012   0.001   PHE B 157 
 TYR   0.011   0.001   TYR B 282 
 ARG   0.003   0.000   ARG B 333 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6859 (mtp180)
REVERT: A  421 LEU cc_start: 0.8181 (mm) cc_final: 0.7885 (mt)
REVERT: B  146 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7271 (tpp-160)
REVERT: B  195 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7658 (t80)
REVERT: B  256 ASP cc_start: 0.7640 (t0) cc_final: 0.7412 (m-30)
REVERT: B  446 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.4845 (t80)
  outliers start: 23
  outliers final: 13
  residues processed: 117
  average time/residue: 0.2425
  time to fit residues: 36.7826
Evaluate side-chains
  106 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 83 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 43 optimal weight:    0.0470
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
B 267 ASN
B 551 GLN
** B 613 GLN ** 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 = 0.4144 r_free = 0.4144 target = 0.172375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.143988 restraints weight = 10138.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.142572 restraints weight = 8237.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.144602 restraints weight = 6724.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7839  Z= 0.157
  Angle     :  0.484  10.715  10680  Z= 0.243
  Chirality :  0.036   0.122   1280
  Planarity :  0.003   0.040   1395
  Dihedral  :  3.403  54.927   1155
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.95 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.26), residues: 1079
  helix:  2.81 (0.18), residues: 733
  sheet: -0.29 (0.80), residues: 51
  loop : -0.12 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.012   0.001   PHE B 588 
 TYR   0.014   0.001   TYR B 428 
 ARG   0.003   0.000   ARG B 252 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  226 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6116 (mtp180)
REVERT: A  269 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7581 (tp)
REVERT: B  146 ARG cc_start: 0.7438 (tpp-160) cc_final: 0.7205 (tpp-160)
REVERT: B  195 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7650 (t80)
REVERT: B  446 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.4836 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2601
  time to fit residues: 38.5543
Evaluate side-chains
  108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0470
   chunk 73 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
B 518 ASN
B 551 GLN
** B 613 GLN ** 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 = 0.4120 r_free = 0.4120 target = 0.170292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.142327 restraints weight = 10134.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.141659 restraints weight = 8398.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.142119 restraints weight = 7006.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7839  Z= 0.174
  Angle     :  0.481   9.053  10680  Z= 0.243
  Chirality :  0.036   0.136   1280
  Planarity :  0.003   0.039   1395
  Dihedral  :  3.391  54.270   1155
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.11 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.26), residues: 1079
  helix:  2.85 (0.18), residues: 733
  sheet: -0.16 (0.80), residues: 51
  loop : -0.05 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.011   0.001   PHE A 207 
 TYR   0.014   0.001   TYR A 408 
 ARG   0.004   0.000   ARG B 333 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6156 (mtp180)
REVERT: A  269 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7583 (tp)
REVERT: A  421 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7989 (tp)
REVERT: B  146 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7238 (tpp-160)
REVERT: B  195 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7614 (t80)
REVERT: B  252 ARG cc_start: 0.7690 (mmt-90) cc_final: 0.7474 (mpt180)
REVERT: B  446 TYR cc_start: 0.5831 (OUTLIER) cc_final: 0.4828 (t80)
  outliers start: 35
  outliers final: 19
  residues processed: 118
  average time/residue: 0.2328
  time to fit residues: 35.9330
Evaluate side-chains
  108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 41 optimal weight:   20.0000
   chunk 12 optimal weight:    0.0170
   chunk 78 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
B 518 ASN
B 551 GLN
** B 613 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.170710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.141904 restraints weight = 10095.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.141082 restraints weight = 7860.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.142305 restraints weight = 6217.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7839  Z= 0.179
  Angle     :  0.494   9.609  10680  Z= 0.247
  Chirality :  0.037   0.165   1280
  Planarity :  0.003   0.038   1395
  Dihedral  :  3.385  53.169   1155
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 24.96 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.26), residues: 1079
  helix:  2.89 (0.19), residues: 733
  sheet: -0.09 (0.81), residues: 51
  loop : -0.04 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.011   0.001   PHE A 207 
 TYR   0.012   0.001   TYR B 282 
 ARG   0.004   0.000   ARG A 467 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6151 (mtp180)
REVERT: A  269 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7513 (tp)
REVERT: A  421 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8045 (tp)
REVERT: B  146 ARG cc_start: 0.7456 (tpp-160) cc_final: 0.7237 (tpp-160)
REVERT: B  195 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7543 (t80)
REVERT: B  446 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.4823 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 116
  average time/residue: 0.2385
  time to fit residues: 36.7784
Evaluate side-chains
  117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 84 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
B 551 GLN
** B 613 GLN ** 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 = 0.4089 r_free = 0.4089 target = 0.167467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.138905 restraints weight = 10141.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.137338 restraints weight = 8451.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.138551 restraints weight = 6772.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7839  Z= 0.255
  Angle     :  0.543  11.692  10680  Z= 0.271
  Chirality :  0.038   0.145   1280
  Planarity :  0.004   0.043   1395
  Dihedral  :  3.566  52.324   1155
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.53 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.26), residues: 1079
  helix:  2.69 (0.19), residues: 733
  sheet: -0.18 (0.81), residues: 51
  loop : -0.17 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 348 
 HIS   0.003   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 207 
 TYR   0.016   0.002   TYR A 408 
 ARG   0.009   0.001   ARG B 252 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 88
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  226 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6350 (mtp180)
REVERT: A  227 ASN cc_start: 0.8111 (m-40) cc_final: 0.7892 (m110)
REVERT: A  461 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (mp)
REVERT: B  195 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7906 (m-80)
REVERT: B  446 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5059 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 113
  average time/residue: 0.2302
  time to fit residues: 34.2767
Evaluate side-chains
  116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 48 optimal weight:   20.0000
   chunk 79 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 518 ASN
** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.169260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.141345 restraints weight = 10178.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.139883 restraints weight = 8241.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.140728 restraints weight = 6563.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7839  Z= 0.193
  Angle     :  0.511  10.759  10680  Z= 0.254
  Chirality :  0.037   0.141   1280
  Planarity :  0.003   0.042   1395
  Dihedral  :  3.474  52.041   1155
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 26.38 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.26), residues: 1079
  helix:  2.80 (0.19), residues: 733
  sheet: -0.10 (0.79), residues: 51
  loop : -0.12 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.011   0.001   PHE A 207 
 TYR   0.012   0.001   TYR B 282 
 ARG   0.008   0.000   ARG B 252 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  226 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6325 (mtp180)
REVERT: A  227 ASN cc_start: 0.8020 (m-40) cc_final: 0.7818 (m110)
REVERT: A  269 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7558 (tp)
REVERT: A  421 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8052 (tp)
REVERT: B  195 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7873 (m-80)
REVERT: B  446 TYR cc_start: 0.6082 (OUTLIER) cc_final: 0.4937 (t80)
  outliers start: 32
  outliers final: 25
  residues processed: 116
  average time/residue: 0.2623
  time to fit residues: 40.2944
Evaluate side-chains
  115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:   50.0000
   chunk 73 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0370
   chunk 67 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 518 ASN
** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.168803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.141072 restraints weight = 10233.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.139605 restraints weight = 8768.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.140691 restraints weight = 6880.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7839  Z= 0.175
  Angle     :  0.506  10.040  10680  Z= 0.252
  Chirality :  0.037   0.139   1280
  Planarity :  0.003   0.040   1395
  Dihedral  :  3.419  51.620   1155
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 26.80 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.26), residues: 1079
  helix:  2.92 (0.19), residues: 728
  sheet:  0.03 (0.78), residues: 51
  loop : -0.09 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.011   0.001   PHE A 207 
 TYR   0.011   0.001   TYR B 282 
 ARG   0.008   0.000   ARG B 333 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 86
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6285 (mtp180)
REVERT: A  269 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7556 (tp)
REVERT: A  421 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8067 (tp)
REVERT: B  195 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7859 (m-80)
REVERT: B  446 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.4884 (t80)
  outliers start: 32
  outliers final: 24
  residues processed: 111
  average time/residue: 0.2679
  time to fit residues: 39.7334
Evaluate side-chains
  113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 97 optimal weight:    0.0770
   chunk 86 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0020
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.4946

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.170976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.143309 restraints weight = 10204.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.141933 restraints weight = 8429.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.143045 restraints weight = 6771.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7839  Z= 0.157
  Angle     :  0.499   9.513  10680  Z= 0.249
  Chirality :  0.036   0.129   1280
  Planarity :  0.003   0.039   1395
  Dihedral  :  3.372  51.041   1155
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 26.80 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.26), residues: 1079
  helix:  3.01 (0.19), residues: 728
  sheet:  0.58 (0.84), residues: 44
  loop : -0.12 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.011   0.001   PHE B 588 
 TYR   0.015   0.001   TYR A 408 
 ARG   0.008   0.000   ARG B 252 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A  226 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6834 (mtp180)
REVERT: A  269 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7503 (tp)
REVERT: A  421 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8072 (tp)
REVERT: B  446 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4724 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 110
  average time/residue: 0.3153
  time to fit residues: 46.0442
Evaluate side-chains
  111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0970
   chunk 76 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 104 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 518 ASN
** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.187597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.154611 restraints weight = 10663.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.158443 restraints weight = 6309.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.161029 restraints weight = 4463.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7839  Z= 0.154
  Angle     :  0.512   9.063  10680  Z= 0.254
  Chirality :  0.036   0.145   1280
  Planarity :  0.003   0.039   1395
  Dihedral  :  2.992  18.207   1153
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 27.22 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.17 (0.26), residues: 1079
  helix:  3.05 (0.19), residues: 728
  sheet:  0.51 (0.88), residues: 39
  loop : -0.07 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.010   0.001   PHE A 339 
 TYR   0.017   0.001   TYR B 541 
 ARG   0.008   0.000   ARG B 252 

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  226 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6728 (mtp180)
REVERT: A  269 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7408 (tp)
REVERT: A  421 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8043 (tp)
REVERT: B  446 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.4809 (t80)
  outliers start: 27
  outliers final: 22
  residues processed: 109
  average time/residue: 0.2585
  time to fit residues: 36.8248
Evaluate side-chains
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  552 GLU
Chi-restraints excluded: chain B residue  571 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0070
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.185143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.152590 restraints weight = 10583.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.156445 restraints weight = 6215.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.158993 restraints weight = 4398.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7839  Z= 0.171
  Angle     :  0.523   9.240  10680  Z= 0.262
  Chirality :  0.037   0.210   1280
  Planarity :  0.003   0.036   1395
  Dihedral  :  2.998  18.236   1153
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 26.66 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.12 (0.26), residues: 1079
  helix:  3.01 (0.19), residues: 728
  sheet:  0.59 (0.89), residues: 39
  loop : -0.09 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.011   0.001   PHE B 588 
 TYR   0.014   0.001   TYR A 408 
 ARG   0.005   0.000   ARG B 252 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3200.31 seconds
wall clock time: 58 minutes 1.23 seconds (3481.23 seconds total)