Starting phenix.real_space_refine
on Wed Mar 12 10:48:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t4g_41030/03_2025/8t4g_41030.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4g_41030/03_2025/8t4g_41030.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/8t4g_41030/03_2025/8t4g_41030.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4g_41030/03_2025/8t4g_41030.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4g_41030/03_2025/8t4g_41030.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4g_41030/03_2025/8t4g_41030.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=   0.028
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    4890      2.51       5
     N    1355      2.21       5
     O    1445      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7721
  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: 4225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4225
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 20, 'TRANS': 530}
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 8
          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: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 79
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG A 529 " occ=0.51
      ... (3 atoms not shown)
      pdb=" CB  ARG A 529 " occ=0.51
  Time building chain proxies: 5.29, per 1000 atoms: 0.69
  Number of scatterers: 7721
  At special positions: 0
  Unit cell: (69.637, 110.748, 132.562, 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    1445      8.00
     N    1355      7.00
     C    4890      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: 1.89
  Conformation dependent library (CDL) restraints added in 1.2 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:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      73.6% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 183 through 202
      removed outlier: 3.871A  pdb=" N   MET A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 218
      removed outlier: 3.993A  pdb=" N   PHE A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 270
      removed outlier: 3.740A  pdb=" N   PHE A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   THR A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A 230 " --> pdb=" O   ARG A 226 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
      removed outlier: 3.570A  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 340
      Proline residue:  A 336  - end of helix
    Processing helix  chain 'A' and resid 340 through 373
      removed outlier: 4.541A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 380
    Processing helix  chain 'A' and resid 382 through 437
      removed outlier: 3.634A  pdb=" N   GLU A 396 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLN A 402 " --> pdb=" O   LYS A 398 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A 403 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A 427 " --> pdb=" O   LYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 476
      removed outlier: 3.714A  pdb=" N   MET A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 3.778A  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 543 through 545
      No H-bonds generated for 'chain 'A' and resid 543 through 545'
    Processing helix  chain 'A' and resid 546 through 552
      removed outlier: 3.842A  pdb=" N   LEU A 550 " --> pdb=" O   THR A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 3.994A  pdb=" N   TYR A 572 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.844A  pdb=" N   ARG A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 644 through 660
    Processing helix  chain 'A' and resid 674 through 688
    Processing helix  chain 'A' and resid 689 through 694
      removed outlier: 3.676A  pdb=" N   ARG A 694 " --> pdb=" O   GLU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 709
      removed outlier: 3.784A  pdb=" N   GLU A 707 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 732
    Processing helix  chain 'A' and resid 734 through 741
    Processing helix  chain 'B' and resid 133 through 145
      removed outlier: 3.557A  pdb=" N   LEU B 137 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 181
      removed outlier: 3.680A  pdb=" N   LEU B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE B 169 " --> pdb=" O   GLY B 165 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 188 through 234
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.592A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 255
    Processing helix  chain 'B' and resid 255 through 260
    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: 4.046A  pdb=" N   LEU B 295 " --> pdb=" O   ARG B 291 " (cutoff:3.500A)
      Proline residue:  B 301  - end of helix
      removed outlier: 3.586A  pdb=" N   GLY B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
    Processing helix  chain 'B' and resid 347 through 402
      removed outlier: 3.604A  pdb=" N   GLU B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B 365 " --> pdb=" O   GLN B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 449
      removed outlier: 3.749A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY B 431 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   TYR B 446 " --> pdb=" O   LYS B 442 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   MET B 447 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG B 449 " --> pdb=" O   SER B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 508
    Processing helix  chain 'B' and resid 509 through 517
      removed outlier: 4.013A  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
      removed outlier: 3.663A  pdb=" N   HIS B 543 " --> pdb=" O   HIS B 539 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER B 544 " --> pdb=" O   CYS B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 572 through 583
    Processing helix  chain 'B' and resid 585 through 590
    Processing helix  chain 'B' and resid 594 through 598
    Processing helix  chain 'B' and resid 601 through 605
    Processing helix  chain 'B' and resid 608 through 622
    Processing helix  chain 'B' and resid 633 through 636
    Processing helix  chain 'B' and resid 638 through 646
    Processing helix  chain 'B' and resid 648 through 653
      removed outlier: 4.765A  pdb=" N   ASP B 653 " --> pdb=" O   ASN B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 668
      removed outlier: 3.820A  pdb=" N   THR B 665 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 524
      removed outlier: 5.880A  pdb=" N   GLN A 522 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   PHE A 510 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A 508 " --> pdb=" O   GLY A 559 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   GLY A 559 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535
      removed outlier: 6.741A  pdb=" N   THR A 534 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 712 through 716
      removed outlier: 6.686A  pdb=" N   ILE A 712 " --> pdb=" O   GLY A 723 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLY A 723 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   PHE A 714 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489
      removed outlier: 5.895A  pdb=" N   LYS B 487 " --> pdb=" O   PHE B 475 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   PHE B 475 " --> pdb=" O   LYS B 487 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL B 473 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 546 through 548
      removed outlier: 6.478A  pdb=" N   VAL B 498 " --> pdb=" O   GLN B 671 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   LEU B 673 " --> pdb=" O   VAL B 498 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   LEU B 675 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   VAL B 502 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)

    586 hydrogen bonds defined for protein.
    1701 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: 2.24

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2615
        1.34 -     1.46: 879
        1.46 -     1.57: 4299
        1.57 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 7846
  Sorted by residual:
  bond pdb=" C   VAL B 547 "
       pdb=" O   VAL B 547 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.014 1.02e-02 9.61e+03 1.83e+00
  bond pdb=" CA  VAL B 547 "
       pdb=" CB  VAL B 547 "
    ideal  model  delta    sigma   weight residual
    1.544  1.526  0.017 1.32e-02 5.74e+03 1.66e+00
  bond pdb=" C   PHE B 195 "
       pdb=" O   PHE B 195 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.015 1.15e-02 7.56e+03 1.63e+00
  bond pdb=" CA  VAL B 467 "
       pdb=" CB  VAL B 467 "
    ideal  model  delta    sigma   weight residual
    1.533  1.547 -0.015 1.14e-02 7.69e+03 1.63e+00
  bond pdb=" C   LEU A 241 "
       pdb=" N   GLU A 242 "
    ideal  model  delta    sigma   weight residual
    1.334  1.318  0.016 1.27e-02 6.20e+03 1.62e+00
  ... (remaining 7841 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 10436
        1.46 -     2.93: 203
        2.93 -     4.39: 34
        4.39 -     5.85: 12
        5.85 -     7.31: 4
  Bond angle restraints: 10689
  Sorted by residual:
  angle pdb=" N   VAL B 485 "
        pdb=" CA  VAL B 485 "
        pdb=" C   VAL B 485 "
      ideal   model   delta    sigma   weight residual
     113.47  109.64    3.83 1.01e+00 9.80e-01 1.44e+01
  angle pdb=" C   PHE B 194 "
        pdb=" N   PHE B 195 "
        pdb=" CA  PHE B 195 "
      ideal   model   delta    sigma   weight residual
     120.65  116.07    4.58 1.32e+00 5.74e-01 1.21e+01
  angle pdb=" CA  GLN A 451 "
        pdb=" CB  GLN A 451 "
        pdb=" CG  GLN A 451 "
      ideal   model   delta    sigma   weight residual
     114.10  120.21   -6.11 2.00e+00 2.50e-01 9.34e+00
  angle pdb=" N   VAL B 419 "
        pdb=" CA  VAL B 419 "
        pdb=" C   VAL B 419 "
      ideal   model   delta    sigma   weight residual
     110.62  113.22   -2.60 1.02e+00 9.61e-01 6.52e+00
  angle pdb=" N   GLU A 242 "
        pdb=" CA  GLU A 242 "
        pdb=" C   GLU A 242 "
      ideal   model   delta    sigma   weight residual
     111.07  108.48    2.59 1.07e+00 8.73e-01 5.84e+00
  ... (remaining 10684 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4153
       17.89 -    35.77: 410
       35.77 -    53.66: 99
       53.66 -    71.54: 12
       71.54 -    89.43: 9
  Dihedral angle restraints: 4683
    sinusoidal: 1562
      harmonic: 3121
  Sorted by residual:
  dihedral pdb=" CA  PHE A 339 "
           pdb=" C   PHE A 339 "
           pdb=" N   LEU A 340 "
           pdb=" CA  LEU A 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP B 237 "
           pdb=" CB  ASP B 237 "
           pdb=" CG  ASP B 237 "
           pdb=" OD1 ASP B 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.40   57.40     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CB  GLU B 351 "
           pdb=" CG  GLU B 351 "
           pdb=" CD  GLU B 351 "
           pdb=" OE1 GLU B 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.56   87.56     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 4680 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 755
       0.027 -    0.054: 346
       0.054 -    0.080: 108
       0.080 -    0.107: 54
       0.107 -    0.134: 15
  Chirality restraints: 1278
  Sorted by residual:
  chirality pdb=" CB  THR A 294 "
            pdb=" CA  THR A 294 "
            pdb=" OG1 THR A 294 "
            pdb=" CG2 THR A 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  MET A 374 "
            pdb=" N   MET A 374 "
            pdb=" C   MET A 374 "
            pdb=" CB  MET A 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ILE A 699 "
            pdb=" N   ILE A 699 "
            pdb=" C   ILE A 699 "
            pdb=" CB  ILE A 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 1275 not shown)

  Planarity restraints: 1397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 567 "    0.041 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 568 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 568 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 568 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 467 "   -0.007 2.00e-02 2.50e+03   1.40e-02 1.97e+00
        pdb=" C   VAL B 467 "    0.024 2.00e-02 2.50e+03
        pdb=" O   VAL B 467 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL B 468 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 672 "   -0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   ILE B 672 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ILE B 672 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU B 673 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1394 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1739
        2.78 -     3.31: 7829
        3.31 -     3.84: 12702
        3.84 -     4.37: 12818
        4.37 -     4.90: 23874
  Nonbonded interactions: 58962
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 338 "
            pdb=" OG  SER A 418 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OE1 GLU B 307 "
            pdb=" OH  TYR B 376 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   GLU B 593 "
            pdb=" OG1 THR B 598 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OD1 ASN B 250 "
            pdb=" OG  SER B 254 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NH1 ARG B 327 "
            pdb=" OE1 GLN B 361 "
     model   vdw
     2.363 3.120
  ... (remaining 58957 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.51 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:             3.230
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.610
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
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   0.026   7846  Z= 0.222
  Angle     :  0.534   7.314  10689  Z= 0.294
  Chirality :  0.038   0.134   1278
  Planarity :  0.003   0.063   1397
  Dihedral  : 15.823  89.430   2673
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 19.35 %
    Favored  : 80.51 %
  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:  2.80 (0.26), residues: 1079
  helix:  2.78 (0.19), residues: 708
  sheet: -0.55 (0.73), residues: 59
  loop :  0.18 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 214 
 HIS   0.012   0.001   HIS B 670 
 PHE   0.009   0.001   PHE B 201 
 TYR   0.010   0.001   TYR B 422 
 ARG   0.002   0.000   ARG A 210 

*********************** 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
  99 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.779 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.2181
  time to fit residues: 28.9603
Evaluate side-chains
  97 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0020
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 83 optimal weight:    0.1980
   chunk 32 optimal weight:   20.0000
   chunk 50 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.169294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.126216 restraints weight = 10304.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.129660 restraints weight = 6018.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.131740 restraints weight = 4331.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3774 r_free = 0.3774    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.0625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7846  Z= 0.163
  Angle     :  0.465   5.838  10689  Z= 0.243
  Chirality :  0.037   0.120   1278
  Planarity :  0.003   0.056   1397
  Dihedral  :  3.943  58.281   1157
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.21 %
    Favored  : 78.53 %
  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:  2.99 (0.27), residues: 1079
  helix:  2.89 (0.19), residues: 718
  sheet: -0.49 (0.72), residues: 58
  loop :  0.27 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 214 
 HIS   0.010   0.001   HIS B 670 
 PHE   0.019   0.001   PHE B 588 
 TYR   0.009   0.001   TYR B 422 
 ARG   0.002   0.000   ARG B 381 

*********************** 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
  115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.782 
Fit side-chains
  outliers start: 16
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1993
  time to fit residues: 30.5319
Evaluate side-chains
  109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.163888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.119706 restraints weight = 10576.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.123047 restraints weight = 6169.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.125192 restraints weight = 4461.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7846  Z= 0.328
  Angle     :  0.544   7.690  10689  Z= 0.280
  Chirality :  0.039   0.141   1278
  Planarity :  0.004   0.050   1397
  Dihedral  :  4.080  56.602   1157
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.77 %
    Favored  : 76.41 %
  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:  2.63 (0.27), residues: 1079
  helix:  2.64 (0.19), residues: 719
  sheet: -0.70 (0.72), residues: 58
  loop :  0.05 (0.39), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 214 
 HIS   0.008   0.002   HIS B 670 
 PHE   0.009   0.001   PHE A 339 
 TYR   0.012   0.002   TYR B 422 
 ARG   0.003   0.000   ARG B 273 

*********************** 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
  117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: B  168 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8361 (mp)
  outliers start: 27
  outliers final: 20
  residues processed: 112
  average time/residue: 0.2175
  time to fit residues: 33.2832
Evaluate side-chains
  111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 103 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 269 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.166596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.121241 restraints weight = 10731.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.124573 restraints weight = 6330.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.126684 restraints weight = 4616.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7846  Z= 0.276
  Angle     :  0.514   7.401  10689  Z= 0.264
  Chirality :  0.038   0.136   1278
  Planarity :  0.003   0.048   1397
  Dihedral  :  3.972  52.066   1157
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.18 %
    Favored  : 74.44 %
  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:  2.66 (0.27), residues: 1079
  helix:  2.67 (0.19), residues: 719
  sheet: -0.78 (0.71), residues: 58
  loop :  0.05 (0.39), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 214 
 HIS   0.008   0.001   HIS B 670 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.014   0.002   TYR B 428 
 ARG   0.002   0.000   ARG B 273 

*********************** 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
  118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: B  404 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8227 (mp)
  outliers start: 24
  outliers final: 20
  residues processed: 114
  average time/residue: 0.2029
  time to fit residues: 31.3498
Evaluate side-chains
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 101 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 29 optimal weight:   20.0000
   chunk 12 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.169669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.124276 restraints weight = 10590.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.127741 restraints weight = 6187.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130034 restraints weight = 4464.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7846  Z= 0.167
  Angle     :  0.471   8.588  10689  Z= 0.239
  Chirality :  0.036   0.124   1278
  Planarity :  0.003   0.047   1397
  Dihedral  :  3.702  51.987   1157
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 22.32 %
    Favored  : 74.01 %
  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:  2.94 (0.27), residues: 1079
  helix:  2.91 (0.19), residues: 719
  sheet: -0.77 (0.70), residues: 58
  loop :  0.11 (0.39), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.010   0.001   PHE B 201 
 TYR   0.009   0.001   TYR B 172 
 ARG   0.002   0.000   ARG A 357 

*********************** 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
  127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: B  404 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8179 (mp)
  outliers start: 26
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1969
  time to fit residues: 33.1238
Evaluate side-chains
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0370
   chunk 68 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0060
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.3074

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.170188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.126664 restraints weight = 10374.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.130251 restraints weight = 5930.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.132506 restraints weight = 4213.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7846  Z= 0.135
  Angle     :  0.461   7.220  10689  Z= 0.233
  Chirality :  0.036   0.123   1278
  Planarity :  0.003   0.046   1397
  Dihedral  :  3.479  51.478   1157
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.58 %
    Favored  : 73.02 %
  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:  3.15 (0.27), residues: 1079
  helix:  3.05 (0.19), residues: 719
  sheet: -0.62 (0.72), residues: 58
  loop :  0.24 (0.40), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 257 
 PHE   0.012   0.001   PHE B 588 
 TYR   0.008   0.001   TYR A 349 
 ARG   0.002   0.000   ARG B 220 

*********************** 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
  120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8004 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 115
  average time/residue: 0.2205
  time to fit residues: 34.2070
Evaluate side-chains
  107 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.4167 r_free = 0.4167 target = 0.167623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.123791 restraints weight = 10450.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.127248 restraints weight = 5994.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.129522 restraints weight = 4286.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7846  Z= 0.209
  Angle     :  0.486   7.579  10689  Z= 0.244
  Chirality :  0.037   0.128   1278
  Planarity :  0.003   0.045   1397
  Dihedral  :  3.472  51.497   1157
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.87 %
    Favored  : 72.74 %
  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:  3.08 (0.27), residues: 1079
  helix:  2.98 (0.19), residues: 721
  sheet: -0.56 (0.74), residues: 58
  loop :  0.20 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 214 
 HIS   0.003   0.001   HIS B 171 
 PHE   0.009   0.001   PHE B 201 
 TYR   0.009   0.001   TYR B 172 
 ARG   0.001   0.000   ARG A 357 

*********************** 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
  120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
REVERT: B  168 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8358 (mp)
REVERT: B  269 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8545 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 117
  average time/residue: 0.2291
  time to fit residues: 36.4120
Evaluate side-chains
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.4164 r_free = 0.4164 target = 0.167417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.123682 restraints weight = 10434.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.127145 restraints weight = 5982.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129331 restraints weight = 4268.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7846  Z= 0.196
  Angle     :  0.487   7.344  10689  Z= 0.245
  Chirality :  0.037   0.125   1278
  Planarity :  0.003   0.044   1397
  Dihedral  :  3.458  51.810   1157
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.58 %
    Favored  : 72.18 %
  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:  3.06 (0.27), residues: 1079
  helix:  2.98 (0.19), residues: 721
  sheet: -0.58 (0.74), residues: 58
  loop :  0.18 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.009   0.001   PHE B 201 
 TYR   0.022   0.001   TYR B 541 
 ARG   0.001   0.000   ARG B 273 

*********************** 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
  117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: B  168 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8359 (mp)
REVERT: B  269 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8515 (t0)
REVERT: B  404 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8102 (mp)
  outliers start: 23
  outliers final: 17
  residues processed: 114
  average time/residue: 0.2048
  time to fit residues: 31.9445
Evaluate side-chains
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:   20.0000
   chunk 48 optimal weight:   40.0000
   chunk 90 optimal weight:    0.7980
   chunk 105 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.4161 r_free = 0.4161 target = 0.167086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.123148 restraints weight = 10618.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.126601 restraints weight = 6059.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.128866 restraints weight = 4317.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7846  Z= 0.206
  Angle     :  0.502   7.272  10689  Z= 0.251
  Chirality :  0.037   0.130   1278
  Planarity :  0.003   0.044   1397
  Dihedral  :  3.455  52.046   1157
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 24.44 %
    Favored  : 71.89 %
  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:  3.05 (0.27), residues: 1079
  helix:  2.97 (0.19), residues: 721
  sheet: -0.56 (0.74), residues: 58
  loop :  0.18 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.009   0.001   PHE B 201 
 TYR   0.010   0.001   TYR B 172 
 ARG   0.002   0.000   ARG A 357 

*********************** 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
  121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 GLU cc_start: 0.8409 (tp30) cc_final: 0.8122 (tp30)
REVERT: B  168 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (mp)
REVERT: B  269 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8493 (t0)
REVERT: B  404 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8085 (mp)
  outliers start: 26
  outliers final: 22
  residues processed: 117
  average time/residue: 0.1973
  time to fit residues: 31.3703
Evaluate side-chains
  120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.4164 r_free = 0.4164 target = 0.167388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.123605 restraints weight = 10434.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.127022 restraints weight = 5990.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.129281 restraints weight = 4282.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7846  Z= 0.196
  Angle     :  0.499   7.168  10689  Z= 0.250
  Chirality :  0.037   0.132   1278
  Planarity :  0.003   0.044   1397
  Dihedral  :  3.448  52.192   1157
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 24.15 %
    Favored  : 72.18 %
  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:  3.08 (0.27), residues: 1079
  helix:  2.99 (0.19), residues: 721
  sheet: -0.56 (0.74), residues: 58
  loop :  0.18 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.009   0.001   PHE B 201 
 TYR   0.009   0.001   TYR B 172 
 ARG   0.001   0.000   ARG A 357 

********************** 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
  124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 GLU cc_start: 0.8388 (tp30) cc_final: 0.8112 (tp30)
REVERT: B  168 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8364 (mp)
REVERT: B  269 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8480 (t0)
REVERT: B  404 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8070 (mp)
  outliers start: 26
  outliers final: 23
  residues processed: 120
  average time/residue: 0.2108
  time to fit residues: 34.6309
Evaluate side-chains
  123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  547 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue    1 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 91 optimal weight:    0.0770
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:   40.0000
   chunk 105 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 50 optimal weight:   20.0000
   overall best weight:    1.1742

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.4141 r_free = 0.4141 target = 0.165097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.121141 restraints weight = 10514.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124534 restraints weight = 6057.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.126632 restraints weight = 4355.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7846  Z= 0.259
  Angle     :  0.532   7.588  10689  Z= 0.267
  Chirality :  0.038   0.131   1278
  Planarity :  0.003   0.044   1397
  Dihedral  :  3.544  52.299   1157
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.01 %
    Favored  : 72.03 %
  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:  2.90 (0.27), residues: 1079
  helix:  2.86 (0.19), residues: 722
  sheet: -0.65 (0.74), residues: 58
  loop :  0.10 (0.40), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 214 
 HIS   0.004   0.001   HIS B 171 
 PHE   0.009   0.001   PHE A 339 
 TYR   0.017   0.002   TYR B 541 
 ARG   0.002   0.000   ARG B 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2776.24 seconds
wall clock time: 49 minutes 31.56 seconds (2971.56 seconds total)